<html><head><meta name="color-scheme" content="light dark"></head><body><pre style="word-wrap: break-word; white-space: pre-wrap;">#!/bin/tcsh
#
# 
#
#####################################################################
# work out what cell cycle/ arrest/cell size regulation/ annotations should be made for long and short cells
# what should the cell cycle phenotype be  and how related to cell size regulation FYPO:0000059 abnormal mitotic cell cycle progression
# all elongated should be some dot of inviable after spore germination (should everything?)
# after updated check lists against advanced query (add to to do list)
# remmeber some cells don't germinate, even for WT
# checks required
# Jacky approve
# check that the description and the substation match
# check that the number of terms in the perl is correct
# check that penetrance and expressivity included whenever possible (and correct!)
# check all ***** removed
# query inviable after spore germination, multiple cell divisions, abnormal morphology (CELL PHENOTYPE)
# has_output microcolony_formation (would want it to be annotated to this, is it?)
# 
# check that population of germinated spores/ is a chile of vegetative population (and the same for cell phenotype)

#####################################################################
# PMID:23697806
# conditions 
# PECO:0000005 standard temperature 25-32
# PECO:0000004 high temperature  (over 32)
# PECO:0000006 low temperature (below 25)
# pentrance 
# high FYPO_EXT:0000001 
# low  FYPO_EXT:0000003
# expressivity 
# high FYPO_EXT:0000001 
# low  FYPO_EXT:0000003

#####################################################################

# 1.
# VIABLE WT cells at 25-32- poor germination
# broad classifier: WT
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology  (high penetrance)
# FYPO:0000582 decreased rate of spore germination (NOT ADDED after discussion with Jacky as not quantified)
# population phenotype
# FYPO:0002060 viable vegetative cell population

echo "1." 
perl -pi -e 's/VIABLE WT cells at 25-32- poor germination/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 2.
# VIABLE small colonies slightly misshapen cells at 32- some misshapen and dead cells  + FYPO:0002273 inviable vegetative cell with abnormal cell morphology
# 
# VIABLE WT cells at 32 cells slightly misshapen at 25,36
# VIABLE slightly misshapen- septated cells- at 25-32
# VIABLE slightly misshapen septated cells at 25-32
# VIABLE slightly misshapen- septated cells at 32
# VIABLE small colonies slightly misshapen cells at 32
# VIABLE small colonies slightly misshapen small cells at 25-32
# VIABLE very small colonies slightly misshapen cells  at 25-32- microcolonies misshapen cells at 36
# VIABLE slightly misshapen septated at 25-32
# 
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (low expressivity) (high penetrance)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population
echo  "2."
perl -pi -e 's/VIABLE small colonies slightly misshapen cells at 32- some misshapen and dead cells/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002273,PECO:0000004,has_penetrance(FYPO_EXT:0000003)| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
# ********* check with Jacky, are dead high t?

perl -pi -e 's/VIABLE WT cells at 32 cells slightly misshapen at 25-36/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE WT cells at 32 cells slightly misshapen at 25/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

perl -pi -e 's/VIABLE slightly misshapen- septated cells- at 25-32/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen septated cells at 25-32/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen- septated cells at 32/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies slightly misshapen cells at 32/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies slightly misshapen small cells at 25-32/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies slightly misshapen cells  at 25-32- microcolonies misshapen cells at 36/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen septated at 25-32/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 3.
# VIABLE WT cells at 32, cells slightly misshapen at 25
# VIABLE WT cells at 32, cells slightly misshapen at 25-36
# broad classifier: misshapen weak viable
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/825/
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (low expressivity) (high penetrance)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population
echo  "3."
perl -pi -e 's/VIABLE WT cells at 32- cells slightly misshapen at 25-36/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE WT cells at 32- cells slightly misshapen at 25/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv



# 3b
# VIABLE slightly misshapen cells 32- some dead cells
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (low expressivity) (high penetrance)
# FYPO:0002273 inviable vegetative cell with abnormal cell morphology (low penetrance)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population
perl -pi -e 's/VIABLE slightly misshapen cells 32- some dead cells/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002273,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv


# 4.
# VIABLE WT cells at 25-32- some dead cells (1)
# broad classifier: WT
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# cell phenotype
# FYPO:0002177 viable cell with normal cell morphology (high penetrance)
# FYPO:0002199 inviable vegetative cell with normal cell morphology (low pentrance)
# poplulation phenotype 
# FYPO:0002060 viable vegetative cell population

echo "4." 
perl -pi -e 's/VIABLE WT cells at 25-32- some dead cells/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002199,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 7.
# VIABLE WT cells at 25,32, many dead cells at 36 (1)  
# remove degrees sign first ******************
# broad classifier WT
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology (high penetrance) (standard temp)
# FYPO:0001489 inviable vegetative cell (medium penetrance) (high temperature)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population  (standard temp)
echo "7."
perl -pi -e 's/VIABLE WT cells at 25-32- many dead cells at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0001489,PECO:0000004,has_penetrance(FYPO_EXT:0000002)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv



# 5.
# VIABLE WT cells at 25-32- many dead cells (1)
# broad classifier: WT
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# cell phenotype
# FYPO:0002177 viable cell with normal cell morphology (high penetrance)
# FYPO:0002199 inviable vegetative cell with normal cell morphology (low pentrance)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population
echo "5." 
perl -pi -e 's/VIABLE WT cells at 25-32- many dead cells/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002199,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 6.
# VIABLE WT cells at 25-32- dead cells causes wavy edges to colony
# broad classifier: WT
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# cell phenotype
# FYPO:0002177 viable cell with normal cell morphology (high penetrance)
# FYPO:0001489 inviable vegetative cell (low penetrance)
# poplulation phenotype
# FYPO:0001404 irregular colony morphology
# FYPO:0002060 viable vegetative cell population
echo "6." 
perl -pi -e 's/VIABLE WT cells at 25-32- dead cells causes wavy edges to colony/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001489,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005| FYPO:0001404,PECO:0000005/g' tab_phenotype.csv


# 8.
# VIABLE WT cells at 25-32" piled up" colony morphology  ******************check quotaions***
# broad classifier WT
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/826/ (piled up colony morphology)
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology (high penetrance)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population
# FYPO:0002296 "piled up" colony morphology
echo "8."
perl -pi -e 's/VIABLE WT cells at 25-32 piled up colony morphology/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002296,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 9.
# VIABLE WT cells at 25,32, poor growth at 36 (leaving out the poor growth, after discussion with Jacky)
# broad classifier WT
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology (high penetrance)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population
echo "9."
perl -pi -e 's/VIABLE WT cells at 25-32- poor growth at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 10.
# VIABLE WT cells at 25,32, possibly poor germination
# broad classifier WT
# cell phenotype
# FYPO:0002177 viable cell with normal cell morphology (high penetrance)
# after discussion with JAcky, ignoring possibly poor germination
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population
echo "10."
perl -pi -e 's/VIABLE WT cells at 25-32- possibly poor germination/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 11.
# VIABLE WT cells at 25,32, longer at 36
# ctu1 WT
# trm10 long high penetrance
# asked Jacky DIFFERENT ********
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology (high penetrance) (standard temperature)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population  (standard temperature)
echo "11."
perl -pi -e 's/VIABLE WT cells at 25-32- longer at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 12.  asked jacky about phenotype at 36 (add this*********)
# VIABLE WT cells with some long cells at 25-32- long cells at 36
# VIABLE small colonies WT with some long cells at 25-32
# VIABLE WT cells some long cells at 25-32
# VIABLE WT cells- some long cells at 25-32
# VIABLE slightly misshapen cells- some long at 32
# VIABLE  small colonies WT cells with some long cells at 32
# VIABLE small colonies WT cells with some long cells at 25-32
# VIABLE WT cells at 25- slightly long cells at 32
# VIABLE very small colonies misshapen septated cells, occasionally long at 25,32 (was misshapen viable in spreadsheet)
# broad classifier: long low penetrance
# cell phenotype
# FYPO:0000059 abnormal mitotic cell cycle progression (low penetrance, standard temp)
# FYPO:0001122  elongated vegetative cell (low penetrance, standard temp)
# population phenotype
# FYPO:0002060 viable vegetative cell population (standard temp)
echo "12."
perl -pi -e 's/VIABLE WT cells with some long cells at 25-32- long cells at 36/FYPO:0000059,PECO:0000005| FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies WT with some long cells at 25-32/FYPO:0000059,PECO:0000005| FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE WT cells some long cells at 25-32/FYPO:0000059| FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE WT cells- some long cells at 25-32/FYPO:0000059,PECO:0000005| FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen cells- some long at 32/FYPO:0000059,PECO:0000005| FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE  small colonies WT cells with some long cells at 32/FYPO:0000059,PECO:0000005| FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies WT cells with some long cells at 25-32/FYPO:0000059,PECO:0000005| FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE WT cells at 25- slightly long cells at 32/FYPO:0000059,PECO:0000005| FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies misshapen septated cells, occasionally long at 25,32/FYPO:0000059,PECO:0000005| FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 13.
# VIABLE WT cells at 25,32, initially slightly misshapen 
# misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (low expressivity)
# population phenotype
# FYPO:0002060 viable vegetative cell population 
echo "13."
perl -pi -e 's/VIABLE WT cells at 25-32- initially slightly misshapen/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003), has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
# how to capture "initially misshapen" **************

# 14.
# VIABLE WT cells at 32- cells slightly misshapen at 25 (1)
# misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (high penetrance) 
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "14."
perl -pi -e 's/VIABLE WT cells at 32- cells slightly misshapen at 25/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 15.
# VIABLE WT cells at 32- cells slightly misshapen at 25 (10)
# misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (high penetrance) (low expressivity)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "15."
perl -pi -e 's/VIABLE WT cells at 32- cells slightly misshapen at 25/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 16.
# VIABLE WT cells at 25-32- slightly misshapen at 36 (1)
# misshapen weak viable
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology  (standard temp) 
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (low expressivity) (high temp)
# population phenotype
# FYPO:0002060 viable vegetative cell population (standard temp)
# FYPO:0002060 viable vegetative cell population (high temp)
echo "16."
perl -pi -e 's/VIABLE WT cells at 25-32- slightly misshapen at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# ***** asked jacky how long stubbiness persists
# 17.
# VIABLE WT cells at 25,32, initially cells look stubby 
# broad classifier stubby
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology  (standard temp) (high penetrance)
# FYPO:0002106 viable stubby vegetative cell 
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population (standard temp)
echo "17."
perl -pi -e 's/VIABLE WT cells at 25-32- initially cells look stubby/FYPO:0002177,PECO:0000005,PECO:0000217,has_penetrance(FYPO_EXT:0000001)| FYPO:0002106,PECO:0000216,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE WT cells at 25-32- initially stubby cells/FYPO:0002177,PECO:0000005,PECO:0000217,has_penetrance(FYPO_EXT:0000001)| FYPO:0002106,PECO:0000216,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 18.
echo "18."

# 19.
# VIABLE WT cells at 25,32, cells misshapen, long, septated at 36
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance? high temp)
# FYPO:0002177 viable cell with normal cell morphology (high penetrance, standard temperature)
# FYPO:0000059 abnormal mitotic cell cycle progression (high temperature)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population (standard temperature)
echo "19."
perl -pi -e 's/VIABLE WT cells at 25-32- cells misshapen- long- septated at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001492,PECO:000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0000059,PECO:000004/g' tab_phenotype.csv

# 20.
# VIABLE long cells at 25-32- cells longer at 36
# long high penetrance
# cell phenotype
# FYPO:0000059 abnormal mitotic cell cycle progression (high penetrance, standard temp)
# FYPO:0001492 elongated viable vegetative cell (high penetrance, standard temp)
# FYPO:0000059 abnormal mitotic cell cycle progression (high penetrance, high expressivity, high temp)
# FYPO:0001492 elongated viable vegetative cell (high penetrance, high expressivity  hightemp)
# population phenotype
# FYPO:0002060 viable vegetative cell population   (standard temp) (867)
# FYPO:0002060 viable vegetative cell population   (high temp high expressivity) (867)
echo "20."
perl -pi -e 's/VIABLE long cells at 25-32- cells longer at 36/FYPO:0000059,PECO:0000005| FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000004| FYPO:0001492,PECO:0000004,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 21
# VIABLE WT cells at 25-32- cells slightly curved at 36
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/839/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# broad classifier: curved
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal morphology (standard temp, high penetrance,) 
# FYPO:0002112 curved viable cell  (high penetrance, low expressivity, high temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population (high temp)  
# FYPO:0002060 viable vegetative cell population (standard temp) 
echo "21."
perl -pi -e 's/VIABLE WT cells at 25-32- cells slightly curved at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002112,PECO:0000004,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000004| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 21b
# VIABLE small colonies long curved cells at 25-32- aberrantly septated
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0002457 viable curved elongated vegetative cell with abnormal septum (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temp)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "21b."
perl -pi -e 's/VIABLE small colonies long curved cells at 25-32- aberrantly septated/FYPO:0002457,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 21c ****Check penetrance*****
# VIABLE curved cells- often aberrantly septated with misplace septum at 25-32
# broad phenotype: curved
# cell phenotype
# FYPO:0002456 viable curved vegetative cell with abnormal septum  https://sourceforge.net/p/pombase/fission-yeast-phenotype/970/
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "21c."
perl -pi -e 's/VIABLE curved cells- often aberrantly septated with misplace septum at 25-32/FYPO:0002456,PECO:0000005 |FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 21d
# VIABLE long branched septated- often curved at 25-32
# VIABLE small colonies long branched septated curved cells at 32
# VIABLE small colonies long branched septated cells at 25-32- cells barely grow at 36
# VIABLE small colonies branched slightly long- septated cells at 25-32- cells almost dead at 36
# broad phenotype: long branched
# cell phenotype 
# FYPO:0002459 viable branched, elongated vegetative cell (viable elongated branched septated)  ( penetrance?**********)
# FYPO:0002460 viable branched, curved, elongated vegetative cell (viable elongated curved branched spetated) ( penetrance?***********)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "21d."
perl -pi -e 's/VIABLE long branched septated- often curved at 25-32/FYPO:0002460,PECO:0000005| FYPO:0002459,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies long branched septated curved cells at 32/FYPO:0002460,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005,/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies long branched septated cells at 25-32- cells barely grow at 36/FYPO:0002459,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies branched slightly long- septated cells at 25-32- cells almost dead at 36/FYPO:0002459,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 22 (see 21)
# VIABLE WT cells at 25,32, cells more curved at 36
# broad classifier: curved
# population
# FYPO:0002060 viable vegetative cell population
echo "22."
perl -pi -e 's/VIABLE WT cells at 25-32- cells more curved at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002112,PECO:0000004,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000004| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 23.
# VIABLE WT cells at 25,32, occasionally slightly curved (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/872/
# broad classifier curved
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal morphology (standard temp, high penetrance,) 
# FYPO:0002112 curved viable cell  (low penetrance, low expressivity, standard temp)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "23."
perl -pi -e 's/VIABLE WT cells at 25-32- occasionally slightly curved/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002112,PECO:0000005,has_penetrance(FYPO_EXT:0000003),has_expressivity(FYPO_EXT:0000003)|  FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 24.
# VIABLE WT cells at 25,32, small colonies curved misshapen cells, often septated at 36
# haven't mentioned septated because these are viable
# curved
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal morphology (standard temp, high penetrance,) 
# FYPO:0002112 curved viable cell  (high temp) (***high penetrance?)
# population phenotype
# FYPO:0002060 viable vegetative cell population (standard temp)
# FYPO:0002060 viable vegetative cell population (high temp)

echo "24."
perl -pi -e 's/VIABLE WT cells at 25-32- small colonies curved misshapen cells- often septated at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002112,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 25.
# VIABLE WT cells at 25,32, cells curved at 36 (1)
# broad classifier: curved
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal morphology (standard temp, high penetrance,) 
# FYPO:0002112 curved viable cell  (high temp) (***high penetrance?)
# population phenotype
# FYPO:0002060 viable vegetative cell population (standard temp)
# FYPO:0002060 viable vegetative cell population (high temp)
echo "25."
perl -pi -e 's/VIABLE WT cells at 25-32- cells curved at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002112,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 25b.
# VIABLE slightly misshapen cells- some curved at 25-32 (low penetrance) (WAS CLASSED AS WEAK MISSHAPEN)
# VIABLE slightly curved cells at 32- cells slightly misshapen at 25
# VIABLE slightly curved cells at 32
# broad classifier: curved
# cell phenotype
# FYPO:0002112 curved viable cell 
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "25."
perl -pi -e 's/VIABLE slightly misshapen cells- some curved at 25-32/FYPO:0002112,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly curved cells at 32- cells slightly misshapen at 25/FYPO:0002112,PECO:0000004,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly curved cells at 32/FYPO:0002112,PECO:0000004,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 26.
# VIABLE WT cells at 32, microcolonies skittle cells at 25
# broad classifier: skittle
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/870/
# cell phenotype
# FYPO:0002110 viable bottle-shaped vegetative cell (standard temperature)
# FYPO:0001315 normal cell morphology during vegetative growth (high temp)
# population phenotype
# FYPO:0002060 viable vegetative cell population (standard temperature)
# FYPO:0002060 viable vegetative cell population  (high temp)
echo "26."
perl -pi -e 's/VIABLE WT cells at 32- microcolonies skittle cells at 25/FYPO:0002110,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001315,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 27a.
# VIABLE small colonies misshapen cells at 25-32- occasionally very long possibly diploidises (add long low pen high express)
# cell phenotype
# FYPO:0001122 elongated vegetative cell (low penetrance 3/ high expressivity)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# FYPO:0001510 viable vegetative cell with abnormal cell shape, normal cell size (high temp) (low expressivity)
# population phenotype
# FYPO:0002060 viable vegetative cell population  (standard temp)
echo "27a."
perl -pi -e 's/VIABLE small colonies misshapen cells at 25-32- occasionally very long possibly diploidises/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 27b.
# VIABLE WT cells at 25,32, small colonies slightly misshapen cells at 36 
# VIABLE small colonies misshapen cells at 25-32
# VIABLE small colonies misshapen- aberrantly septated at 25-32 (PLUS abnormal septation)
# broad classifier: misshapen viable
# cell phenotype
# FYPO:0001315 normal cell morphology during vegetative growth (standard temp) (high penetrance)
# FYPO:0001510 viable vegetative cell with abnormal cell shape, normal cell size (high temp) (low expressivity)
# population phenotype
# FYPO:0002060 viable vegetative cell population   (standard temp)
# FYPO:0002060 viable vegetative cell population   (high temp)

echo "27b."
perl -pi -e 's/VIABLE WT cells at 25-32- small colonies slightly misshapen cells at 36/FYPO:0001315,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies misshapen cells at 25-32/FYPO:0001315,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies misshapen- aberrantly septated at 25-32/FYPO:0001315,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000117,PECO:0000005|  FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE  small colonies misshapen cells possibly reverting to give larger colonies slightly misshapen cells at 32- germinated spores at 25/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 28.
# VIABLE WT cells at 25,32, slightly long at 36 (1)
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal morphology  (standard temp)
# FYPO:0001492 elongated viable vegetative cell (high penetrance) (high temp) (low expressivity)
# FYPO:0000059 abnormal mitotic cell cycle progression (high temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population  (standard temp)
# FYPO:0002060 viable vegetative cell population   (high temp) 
echo "28."
perl -pi -e 's/VIABLE WT cells at 25-32- slightly long at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001492,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000004| FYPO:0002060,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 29.
# VIABLE WT cells at 25,32, cells stubby  at 36 (1)
# VIABLE WT cells at 25- slightly misshapen cells at 32- stubby cells at 36
# broad classifier: stubby
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal morphology (standard temp, high penetrance) 
# FYPO:0002106 viable stubby vegetative cell  (high temp) (**********high penetrance?)
# population phenotype
# FYPO:0002060 viable vegetative cell population (standard temp)
# FYPO:0002060 viable vegetative cell population (high temp)
echo "29."
perl -pi -e 's/VIABLE WT cells at 25-32- cells stubby at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002106,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE WT cells at 25-32- cells stubby  at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002106,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE WT cells at 25- slightly misshapen cells at 32- stubby cells at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002106,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 30. (ask jacky, what expressivity)
# VIABLE long cells at 32, WT cells at 25 
# long high penetrance
# FYPO:0002177 viable vegetative cell with normal morphology (standard temp, high penetrance,) 
# FYPO:0001492 viable elongated vegetative cell  (high temp) (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (high temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population (standard temp)
# FYPO:0002060 viable vegetative cell population  (high temp)
echo "30."
perl -pi -e 's/VIABLE long cells at 32- WT cells at 25/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001492,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000004| FYPO:0002060,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 31.
# VIABLE very small colonies rounded cells at 25,32, lysis after 48h (****Add after 48 hours)(****what penetrance for lysis???)
# rounded
# cell phenotype
# FYPO:0000946 normal volume spheroid vegetative cell
# FYPO:0000647 vegetative cell lysis 
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "31."
perl -pi -e 's/VIABLE very small colonies rounded cells at 25-32- lysis after 48h/FYPO:0000946,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000647,PECO:0000005,PECO:0000237| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 32.
# VIABLE slightly curved cells at 25,32, many misshapen cells on exit from stationary phase
# broad classifier: curved
# cell phenotype 
# FYPO:0002112 curved viable cell  (low expressivity)  (high penetrance)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "32."
perl -pi -e 's/VIABLE slightly curved cells at 25-32- many misshapen cells on exit from stationary phase/FYPO:0002112,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 33.
# VIABLE slightly misshapen cells at 32- small colonies rounded cells at 25 (1)
# broad classifier: rounded
# cell phenotype
# FYPO:0002380 viable  spheroid vegetative cell  (high_penetrance) 
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "33."
perl -pi -e 's/VIABLE slightly misshapen cells at 32- small colonies rounded cells at 25/FYPO:0002380,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# Asked Jacky about penetrnace of curved (add qualifier and pop term)*************and if also elongated
# 34.
# ESSENTIAL microcolonies long cells at 25,32, curved misshapen cells at 36 (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/793/
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell, interphase block (high penetrance) (high expressivity) (standard temp)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# FYPO:0002113 inviable curved vegetative cell (high temp)
# population phenotype
# FYPO:0002061 inviable vegetative cell population (standard temp)
echo "34."
perl -pi -e 's/ESSENTIAL microcolonies long cells at 25-32- curved misshapen cells at 36/FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|  FYPO:0002113,PECO:0000004| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv


# 35.
# ESSENTIAL microcolonies long cells at 25,32, grows better at 25
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell, interphase block  (high penetrance) (high expressivity) (standard temp)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002061 inviable vegetative cell population (standard temp)
echo "35"
perl -pi -e 's/ESSENTIAL microcolonies long cells at 25-32- grows better at 25/FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|  FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 36.
# VIABLE slightly misshapen cells at 25,32, some colonies misshapen cells and lysis at 36
# misshapen weak viable
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (high penetrance, low expressivity, standard temp) 
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (low penetrance, low expressivity, high temp) 
# FYPO:0000647 cell lysis (low penetrance, high temp) 
# population phenotype
# FYPO:0002060 viable vegetative cell population (standard temp)
echo "36."
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32- some colonies misshapen cells and lysis at 36/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0001510,PECO:0000004,has_penetrance(FYPO_EXT:0000003),has_expressivity(FYPO_EXT:0000003)| FYPO:0000647,PECO:0000004,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 37.
# VIABLE slightly misshapen cells at 32- very small colonies slightly misshapen cells at 25 (1)
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (high penetrance, low expressivity) 
# population phenotype
# FYPO:0002060 viable vegetative cell population 
echo "37."
perl -pi -e s'/VIABLE slightly misshapen cells at 32- very small colonies slightly misshapen cells at 25/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005,/g' tab_phenotype.csv

# 38.
# VIABLE slightly misshapen cells at 32- cells misshapen at 25 (1)
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (high penetrance, low expressivity) 
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "38."
perl -pi -e s'/VIABLE slightly misshapen cells at 32- cells misshapen at 25/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005,/g' tab_phenotype.csv

# 40.
# VIABLE long cells at 25,32, cells longer mostly inviable at 36  (1)
# long high penetrance
# FYPO:0001492 viable elongated vegetative cell  (standard temp) (high penetrance)
# FYPO:0001490 inviable elongated vegetative cell  (high temp) (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population (standard temp)
echo "40."
perl -pi -e 's/VIABLE long cells at 25-32- cells longer mostly inviable at 36/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0001490,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 41.
# ESSENTIAL microcolonies skittle cells at 25,32 ,larger colonies at 25
# skittle
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/808/
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell (high penetrance)
# cell population phenotype
# FYPO:0002061 inviable vegetative cell population /808/
echo "41."
perl -pi -e 's/ESSENTIAL microcolonies skittle cells at 25-32 -larger colonies at 25/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv


# 42a.
# VIABLE slightly misshapen cells at 32, cells more WT at 25 (1)
# broad classifier: misshapen weak viable
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/825/
# cell phenotype
# FYPO:0001510 viable vegetative cell with abnormal cell shape, normal cell size (low expressivity)
# population phenotype
# FYPO:0002060 viable vegetative cell population 
echo "42a."
perl -pi -e 's/VIABLE slightly misshapen cells at 32- cells more WT at 25/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 42b.
# VIABLE slightly misshapen cells at 25,32, cells initially misshapen from germination  (1) 
# broad classifier: misshapen weak viable
# https://sourceforge.net/pombase/fission-yeast-phenotype/825/
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (low expressivity) (high penetrance)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population 
echo "42b."
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32- cells initially misshapen from germination/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# ***** asked JAcky about penetrance of long
# 42c.
# VIABLE slightly misshapen cells at 25,32, cells long misshapen at 36
# broad classifier: misshapen weak viable
# https://sourceforge.net/pombase/fission-yeast-phenotype/825/
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (low expressivity) (high penetrance)
# FYPO:0001492 viable elongated vegetative cell  (high temp) (???????******* penetrance)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population 
echo "42c."
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32- cells long misshapen at 36/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0001492,PECO:0000004| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 42d.
# VIABLE slightly misshapen cells at 25,32, ESSENTIAL long misshapen cells at 36 (1) 
# misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (low expressivity) (high penetrance) (standard temp)
# FYPO:0001490 inviable elongated vegetative cell  (high temp) (???????******* penetrance)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population  (standard temp)
echo "42d."
perl -pi -e 's/VIABLE slightly misshapen cells at 25,32, ESSENTIAL long misshapen cells at 36/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0001490,PECO:0000004| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 42e. 
# VIABLE slightly misshapen cells at 25,32, branched misshapen cells at 36 (1)
# broad classifier: misshapen weak viable (was classed as misshapen viable in paper?)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/825/
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (low expressivity) (high penetrance) (standard temp)
# FYPO:0000015 (branched vegetative cell) at high temperature
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population (standard temp)
echo "42e."
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32- branched misshapen cells at 36/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0000015,PECO:0000004| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 42f.
# VIABLE slightly misshapen cells at 25,32,  cells misshapen at 36
# broad classifier: misshapen viable
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/825/
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (low expressivity)  (high pen) (standard temp) 
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (high expressivity)   (high pen)  (high temp)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population (standard temp) (high temp)
echo "42f."
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32-  cells misshapen at 36/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000001),has_penetrance(FYPO_EXT:0000001)| FYPO:0000015,PECO:0000004| FYPO:0002060,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 42g.
# VIABLE slightly misshapen cells at 25,32, some long cells at 36
# broad classifier: misshapen weak viable
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/825/
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (low expressivity)  (high pen) (standard temp) 
#  viable elongated vegetative cell (low pen)  (high temp)
# FYPO:0001122 phenotype
# FYPO:0002060 viable vegetative cell population (standard temp) 
echo "42g."
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32- some long cells at 36/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0001122,PECO:0000006,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 43.
# VIABLE small colonies long cells at 25,32, occasionally aberrantly septated with misplaced septum
# VIABLE small colonies slightly long cells at 32 (add low specificity)
# VIABLE small colonies slightly long cells at 32- cells slightly misshapen at 25
# long high penetrance
# FYPO:0001492 viable elongated vegetative cell  (standard temp) (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population (standard temp)
# FYPO:0000339 mislocalized septum (low penetrance)
echo "43."
perl -pi -e 's/VIABLE small colonies long cells at 25-32- occasionally aberrantly septated with misplaced septum/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004| FYPO:0000339,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies slightly long cells at 32- cells slightly misshapen at 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies slightly long cells at 32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 44. 
echo "44."

# 45 
# VIABLE long cells at 32, microcolonies long cells at 25 
# VIABLE small colonies long slightly misshapen cells at 25-32
# VIABLE very small colonies long cells at 32, small colonies long cells at 25.
# VIABLE very small colonies long cells at 32
# long high penetrance
# cell phenotype
# FYPO:0001492 viable elongated vegetative cell  (standard temp) (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population  (standard temp)
echo "45."
perl -pi -e 's/VIABLE long cells at 32- microcolonies long cells at 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies long slightly misshapen cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies long cells at 32- small colonies long cells at 25./FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies long cells at 32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 46.
# VIABLE long cells at 32, cells slightly long at 25 (1)
# long high penetrance
# cell phenotype
# FYPO:0001492 viable elongated vegetative cell  (standard temp) (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population  (standard temp)
echo "46."
perl -pi -e 's/VIABLE long cells at 32- cells slightly long at 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 47.
# VIABLE small colonies long cells at 25,32, lots of dead cells (1)
# long high penetrance
# cell phenotype
# FYPO:0001492 viable elongated vegetative cell  (standard temp) (high penetrance)
# FYPO:0001490 inviable elongated vegetative cell (standard temp) (low penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (high temperature)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population (standard temp)
echo "47."
perl -pi -e 's/VIABLE small colonies long cells at 25-32- lots of dead cells/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000004| FYPO:0000059,PECO:0000005| FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
# check this with jacky supressors *****************are the dead cells elongated?

# 48. 
echo "48"

# 49.
# VIABLE slightly long cells at 32, small colonies long cells at 25 (1)
# long high penetrance
# cell phenotype
# FYPO:0001492 viable elongated vegetative cell  (standard temp) (high penetrance)
# FYPO:0001492 viable elongated vegetative cell  (high temp) (high penetrance) (low expessivity)
# FYPO:0000059 abnormal mitotic cell cycle progression (high temperature)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population  (standard temp)
echo "49."
perl -pi -e 's/VIABLE slightly long cells at 32- small colonies long cells at 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001492,PECO:0000004,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000004| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 50. 
echo "51."
# *****ask Jacky about penetracne
# 51. 
# ESSENTIAL swollen spores at 25,32 some germinated spores at 25 (misshapen essential in paper)
# broad classifier: spores 
# cell phenotype
# FYPO:0002207 inviable swollen spore (standard temp)
# FYPO:0002207 inviable swollen spore (low temp)
# FYPO:0001991 inviable after spore germination, without cell division germinated spores (low temp)
# population phenotype
# FYPO:0002061 inviable vegetative cell population (standard temp)
# FYPO:0002061 inviable vegetative cell population (low temp)
echo "51."
perl -pi -e 's/ESSENTIAL swollen spores at 25-32 some germinated spores at 25/FYPO:0002207,PECO:0000005| FYPO:0002207,PECO:0000006| FYPO:0001991,PECO:0000006| FYPO:0002061,PECO:0000005| FYPO:0002061,PECO:0000006/g' tab_phenotype.csv

# 52. 
# VIABLE long cells at 32, cells not long but often curved at 25 (1)
# long high penetrance
# cell phenotype
# FYPO:0001492 viable elongated vegetative cell  (standard temp) (high penetrance)
# FYPO:0002112 viable curved vegetative cell (low temp)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population  (standard temp)
echo "52."
perl -pi -e 's/VIABLE long cells at 32- cells not long but often curved at 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002112,PECO:0000006| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 53.
# VIABLE slightly misshapen cells at 25,32, rounded cells at 36
# broad classifier:  rounded 
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/825/
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (low expressivity) (high penetrance) (standard temp)
# FYPO:0002380 viable spheroid vegetative cell (high temp)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population (standard temp)
# FYPO:0002060 viable vegetative cell population  (high temp)
echo "53."
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32- rounded cells at 36/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002380,PECO:0000004| FYPO:0002060,PECO:0000004| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 54.
# VIABLE slightly misshapen cells at 32, more septated cells at 25 (1)
# VIABLE small colonies misshapen- septated cells at 25-32
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell with abnormal cell shape, normal cell size (low expressivity)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "54."
perl -pi -e 's/VIABLE slightly misshapen cells at 32- more septated cells at 25/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies misshapen- septated cells at 25-32/FYPO:0001510,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

echo "55."
echo "56."
echo "57."
echo "58."

# 59. 
# ESSENTIAL microcolonies misshapen cells at 25-32
# broad classifier: misshapen essential
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/831/
# cell phenotype
# FYPO:0002148 inviable after spore germination, multiple cell divisions, abnormal morphology (high_penetrance)
# population phenotype 
# FYPO:0002061 inviable vegetative cell population
# echo "59."
perl -pi -e 's/ESSENTIAL microcolonies misshapen cells at 25-32/FYPO:0002148,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 60.  
# ESSENTIAL microcolonies small cells at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/779
# cell phenotype
# FYPO:0000951 small inviable vegetative cell (High penetrance) 
# population phenotype
# FYPO:0002061 inviable vegetative cell population 
echo "60."
perl -pi -e 's/ESSENTIAL microcolonies small cells at 25-32/FYPO:0000951,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 61. 
# ESSENTIAL microcolonies rounded cells at 25-32 (29)
# ESSENTIAL microcolonies slightly rounded cells at 25-32 (low expressivity)
# ESSENTIAL microcolonies rounded cells- lysis at 25- spores at 32  + FYPO:0000647
# broad classifier: rounded 
# cell phenotype
# FYPO:0002187 inviable normal volume spheroid vegetative cell   (high penetrance)  
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "61."
perl -pi -e 's/ESSENTIAL microcolonies rounded cells at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies slightly rounded cells at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies rounded cells- lysis at 25- spores at 32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005| FYPO:0000647,PECO:0000006/g' tab_phenotype.csv

# 62. 
# ESSENTIAL microcolonies rounded cells at 32 cells slightly misshapen at 25 (1)
# broad classifier: rounded 
echo "62."
perl -pi -e 's/ESSENTIAL microcolonies rounded cells at 32 cells slightly misshapen at 25/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 63. 
# ESSENTIAL microcolonies rounded cells at 32 colonies larger at 25 (1)
# broad classifier: rounded 
echo "63."
perl -pi -e 's/ESSENTIAL microcolonies rounded cells at 32 colonies larger at 25/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 64. 
# ESSENTIAL microcolonies rounded cells at 32- cells more WT at 25 (1)
# broad classifier: rounded 
echo "64."
perl -pi -e 's/ESSENTIAL microcolonies rounded cells at 32- cells more WT at 25/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 65
# ESSENTIAL microcolonies  rounded cells at 25-32 (4)
# broad classifier: rounded 
echo  "65."
perl -pi -e 's/ESSENTIAL microcolonies  rounded cells at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 66.
# ESSENTIAL microcolonies rounded cells- colonies appear dark at 25-32 (1) 
# broad classifier: rounded 
# cellular phenotype 
# FYPO:0000741 increased cellular pigment accumulation (additional cellular phenotype)
# population phenotype 
# FYPO:0002061 inviable vegetative cell population
echo "66."
perl -pi -e 's/ESSENTIAL microcolonies rounded cells- colonies appear dark at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000741,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 67.
# ESSENTIAL microcolonies slightly rounded cells appear to be dark edged at 25-32 (1) 
# broad classifier: rounded 
# cellular phenotype
# plus (low expressivity) for FYPO:***** inviable normal volume spheroid vegetative cell  (high penetrance) 
# plus FYPO:0000741 increased cellular pigment accumulation
# population phenotype 
# FYPO:0002061 inviable vegetative cell population
echo  "67."
perl -pi -e 's/ESSENTIAL microcolonies slightly rounded cells appear to be dark edged at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000741,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 68.
# ESSENTIAL microcolonies slightly misshapen rounded cells at 25-32  (1)  
# broad classifier: rounded 
# cellular phenotype
# plus (low expressivity) for  for FYPO:***** inviable normal volume spheroid vegetative cell  (high penetrance) 
# population phenotype 
# FYPO:0002061 inviable vegetative cell population
echo "68."
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen rounded cells at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 69.
# ESSENTIAL microcolonies slightly rounded cells at 25-32 (1)
# broad classifier: rounded 
# cellular phenotype
# plus expressivity low for FYPO:***** inviable normal volume spheroid vegetative cell  (high penetrance) 
# population phenotype 
# FYPO:0002061 inviable vegetative cell population
echo "69"
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen rounded cells at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 70.
# ESSENTIAL microcolonies rounded cells- lysis at 25- spores at 32 (1)
# broad classifier: rounded 
# cell phenotype
# FYPO:0002187 inviable normal volume spheroid vegetative cell  (high penetrance)  (low temp)
# FYPO:0000647 cell lysis (low temp)
# *********plus spores (high temperature)
# population phenotype 
# FYPO:0002061 inviable vegetative cell population 
echo "70."
perl -pi -e 's/ESSENTIAL microcolonies rounded cells at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000647,PECO:0000006| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 71
# ESSENTIAL microcolonies rounded cells- lysis at 25-32  (3) 
# broad classifier: rounded
# cell phenotype
# plus FYPO:0000647 cell lysis
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "71."
perl -pi -e 's/ESSENTIAL microcolonies rounded cells- lysis at 25-32/FYPO:0000951,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000647,PECO:0000005 | FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 72. 
# ESSENTIAL germinated spores- microcolonies rounded cells at 25-32 (1)
# broad classifier: rounded
# cell phenotype
# FYPO:0000021 inviable spheroid vegetative cell 
# FYPO:0000310 inviable after spore germination with normal germ tube morphology 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
# JAcky can't recall penetrance so leaving this
echo "72."
perl -pi -e 's/ESSENTIAL germinated spores- microcolonies rounded cells at 25-32/FYPO:0000021,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv


# 73.
# ESSENTIAL spores- germinated spores- microcolonies rounded cells at 25-32 (1)
# broad classifier: rounded
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/837/
# cell phenotype
# FYPO:0000021 inviable spheroid vegetative cell
# FYPO:0000310 inviable after spore germination with normal germ tube morphology
# FYPO:0002151 inviable spore
# cell population phenotype
# FYPO:0002061 inviable vegetative cell population
# penetrance Jacky not sure so leaving
echo "73."
perl -pi -e 's/ESSENTIAL spores- germinated spores- microcolonies rounded cells at 25-32/FYPO:0000021,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000310,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 74. 
# ESSENTIAL germinated spores misshapen at 25,32, germinated spores occasionally long at 25
# ESSENTIAL germinated spores misshapen- occasionally long at 25-32
# ESSENTIAL germinated spores long misshapen- septated at 32- microcolonies long cells at 25 
# ESSENTIAL germinated spores long- often misshapen at 32- spores some germination at 25 (long high pen)
# broad classifier: misshapen essential
# cell phenotype
# FYPO:0000313 inviable after spore germination with abnormal germ tube morphology (standard temp)
# FYPO:0002379 inviable after spore germination with elongated germ  (low pen) (low temp)
# population phenotype
# FYPO:0002061 inviable vegetative cell population  (standard temp)
echo "74."
perl -pi -e 's/ESSENTIAL germinated spores misshapen at 25-32- germinated spores occasionally long at 25/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001) |FYPO:0002379,PECO:0000006,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores misshapen- occasionally long at 25-32/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002379,PECO:0000006,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores long misshapen- septated at 32- microcolonies long cells at 25/FYPO:0002379,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores long- often misshapen at 32- spores some germination at 25/FYPO:0002379,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 75.
# ESSENTIAL germinated spores misshapen at 25-32
# ESSENTIAL germinated spores misshapen- occasionally microcolonies septated cells at 25-32
# broad classifier: misshapen essential
# cell phenotype
# FYPO:0000313 inviable after spore germination with abnormal germ tube morphology
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "75."
perl -pi -e 's/ESSENTIAL germinated spores misshapen at 25-32/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores misshapen- occasionally microcolonies septated cells at 25-32/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 76.
# VIABLE slightly stubby cells at 25,32, cells more stubby at 36
# VIABLE slightly stubby cells at 25,32, cells seem to die rapidly in stationary phase
# VIABLE slightly stubby cells at 25,32
# broad classifier:  stubby
# cell phenotype
# FYPO:0002106 stubby viable cell  (low expressivity) (high penetrance)
# population phenotype
# FYPO:0002060 viable vegetative cell population
# FYPO:0000245 loss of viability in stationary phase (population phenotype)
echo "76."
perl -pi -e 's/VIABLE slightly stubby cells at 25-32- cells more stubby at 36/FYPO:0002106,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly stubby cells at 25-32- cells seem to die rapidly in stationary phase/FYPO:0002106,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0000245,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly stubby cells at 25-32/FYPO:0002106,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

echo "no 77-82."

# 83. 
# ESSENTIAL spores  at 25-32
# ESSENTIAL spores at 32- spores- occasionally germinated spores long at 25
# broad classifier: spores
# cell phenotype
# FYPO:0002151 inviable spore  (high penetrance)
# FYPO:0002379 inviable after spore germination, without cell division, with elongated germ tube (low penetrance)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "83"
perl -pi -e 's/ESSENTIAL spores  at 25-32/FYPO:0002061,PECO:0000005| FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000001)/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores at 32- spores- occasionally germinated spores long at 25/FYPO:0002061,PECO:0000005| FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002379,PECO:0000006,has_penetrance(FYPO_EXT:0000003)/g' tab_phenotype.csv

# 84a. 
# VIABLE slightly curved cells at 25,32, occasionally cells are T-shaped
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/839/
# broad classifier: curved
# cell phenotype 
# FYPO:0002112 curved viable cell  (low expressivity)  (high penetrance)
# FYPO:0000013 T-shaped cell (low penetrance)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "84a"
perl -pi -e 's/VIABLE slightly curved cells at 25-32- occasionally cells are T-shaped/FYPO:0002112,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000003)| FYPO:0000013,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 84b. 
# VIABLE slightly curved cells at 25,32
# VIABLE small colonies slightly curved cells at 25-32- cells more curved at 36
# VIABLE slightly misshapen- slightly curved cells at 25-32-  cells misshapen at 36
# broad classifier: curved
# cell phenotype
# FYPO:0002112 curved viable cell  (low expressivity)  (high penetrance)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "84b"
perl -pi -e 's/VIABLE slightly curved cells at 25-32/FYPO:0002112,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies slightly curved cells at 25-32- cells more curved at 36/FYPO:0002112,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen- slightly curved cells at 25-32-  cells misshapen at 36/FYPO:0002112,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 85.
# ESSENTIAL small colonies skittle cells at 25-32
# broad classifier: skittle
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell 
# population phenoype
# FYPO:0002061 inviable vegetative cell population
echo "85."
perl -pi -e 's/ESSENTIAL small colonies skittle cells at 25-32/FYPO:0002111,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 86.
# ESSENTIAL microcolonies skittle cells- small colonies WT cells at 25-32 (38)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/840/
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/803/
# broad classifier: skittle
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell
# FYPO:0002199 inviable vegetative cells with normal morphology (840)
# population phenoype
# FYPO:0002061 inviable vegetative cell population
echo "86."
perl -pi -e 's/ESSENTIAL microcolonies skittle cells- small colonies WT cells at 25-32/FYPO:0002111,PECO:0000005| FYPO:0002199,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 87a. 
# VIABLE small colonies slightly misshapen cells at 25,32, cells swollen, misshapen at 36
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/812/
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0002402 viable swollen vegetative cell with abnormal cell shape (high temperature) (high penetrance?) 
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (low expressivity)  (standard temp) (high penetrance)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "87.a"
perl -pi -e 's/VIABLE small colonies slightly misshapen cells at 25-32- cells swollen- misshapen at 36/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002402,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 87b. 
# VIABLE small colonies slightly misshapen cells at 25-32
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (low expressivity) (high expressivity?)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "87.b"
perl -pi -e 's/VIABLE small colonies slightly misshapen cells at 25-32/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 87.c.
# broad classifier: rounded
# VIABLE very small colonies rounded cells at 25-32
# cell phenotype
# FYPO:0000946 normal volume spheroid vegetative cell
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "87.c."
perl -pi -e 's/VIABLE very small colonies rounded cells at 25-32/FYPO:0000946,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 88. 
# VIABLE WT cells at 32
# cell phenotype
# FYPO:0002177 viable cell with normal morphology (high penetrance)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "88."
perl -pi -e 's/VIABLE WT cells at 32/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 89.
# VIABLE small colonies WT cells at 25,32, some larger colonies after 2 days at 32 possibly suppressors
# VIABLE small colonies WT cells at 25-32
# broad classifier: WT
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology   (high penetrance)
# population phenotype 
# FYPO:0002060 viable vegetative cell population 
echo "89."
perl -pi -e 's/VIABLE small colonies WT cells at 25-32- some larger colonies after 2 days at 32 possibly suppressors/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies WT cells at 25-32/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 89b.
# VIABLE small colonies long cells at 25,32 many longer cells possibly diploidising (1) (add diploidising)
# VIABLE small colonies long cells at 25,32, possibly diploidising at high frequency (1) (add diploidising)
# long high penetrance
# FYPO:0000059 abnormal mitotic cell cycle progression 
# FYPO:0001492 elongated viable vegetative cell (high penetrance) 
# population phenotype
# FYPO:0002060 viable vegetative cell population (standard temp) 
echo "89b."
perl -pi -e 's/VIABLE small colonies long cells at 25-32 many longer cells possibly diploidising/FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005| FYPO:0001492,PECO:0000004,has_penetrance(FYPO_EXT:0000001)/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies long cells at 25-32- possibly diploidising at high frequency/FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005| FYPO:0001492,PECO:0000004,has_penetrance(FYPO_EXT:0000001)/g' tab_phenotype.csv

# ************ask jacky about penetrance of curved
# 90a. 
# VIABLE small colonies long cells at 25,32, cells curved  aberrantly septated with misplaced septum at 36
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance) (standard temp)
# FYPO:0000059 abnormal mitotic cell cycle progression
# FYPO:0002115 viable curved elongated vegetative cell (high temp) (high pen) 
# FYPO:0000339 mislocalized septum  (high temp)
# population phenotype
# FYPO:0002060 viable vegetative cell population (standard temp) 
echo "90a"
perl -pi -e 's/VIABLE small colonies long cells at 25-32- cells curved  aberrantly septated with misplaced septum at 36/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005| FYPO:0002115,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0000339,PECO:0000004/g' tab_phenotype.csv


# 90b. 
# VIABLE small colonies long cells at 25,32
# VIABLE very small colonies long misshapen cells at 32- 25
# VIABLE long cells at 25- microcolonies long misshapen cells at 32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/786/
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "90b"
perl -pi -e 's/VIABLE small colonies long cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies long misshapen cells at 32- 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE long cells at 25- microcolonies long misshapen cells at 32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv


# 91.
# ESSENTIAL microcolonies slightly misshapen cells- some long cells at 25-32
# broad classifier: long low penetrance
# cell phenotype 
# FYPO:0001490 elongated inviable vegetative cell (low penetrance)
# FYPO:0001511 inviable vegetative cell, abnormal cell shape, normal cell size   (high_penetrance/ low expressivity) 
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# cell population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "91."
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells- some long cells at 25-32/FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0001511,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000004| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv 

# 92.
# ESSENTIAL microcolonies slightly misshapen cells at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/831/
# broad classifier: essential misshapen
# cell phenotype
# FYPO:0001511 inviable vegetative cell, abnormal cell shape, normal cell size (high_penetrance/ low expressivity) 
# population phenotype
# FYPO:0002061 viable vegetative cell population
echo "92."
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells at 25-32/FYPO:0001511,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 93a. 
# ESSENTIAL microcolonies long cells at 25,32, cells longer at 25
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/793/
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell, interphase block (high penetrance) (high expressivity)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "93 a."
perl -pi -e 's/ESSENTIAL microcolonies long cells at 25-32- cells longer at 25/FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 93 b. 
# ESSENTIAL microcolonies long cells at 25-32
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell, interphase block (high penetrance) (high expressivity)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "93 b."
perl -pi -e 's/ESSENTIAL microcolonies long cells at 25-32/FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 94a. 
# VIABLE WT cells with some long cells at 25,32, aberrantly septated at 36 
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/841/
# broad classifier: long low penetrance
# cell phenotype
# FYPO:0002104 viable cell with normal cell shape (high penetrance 1)
# FYPO:0001122 elongated viable vegetative cell (low penetrance 3)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# FYPO:0000117 abnormal septation (high temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "94a."
perl -pi -e 's/VIABLE WT cells with some long cells at 25-32-  aberrantly septated at 36/FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002104,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0000117,PECO:0000004| FYPO:0000059,PECO:0000004| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv


# 94b. 
# VIABLE WT cells with some long cells at 25,32 
# VIABLE WT cells occasionally long at 25-32 (classed as long high pen in spreadsheet!!!!)
# VIABLE very small colonies WT cells with some long cells  at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/841/
# broad classifier: long low penetrance
# cell phenotype
# FYPO:0002104 viable cell with normal cell shape (high penetrance 1)
# FYPO:0001122 elongated viable vegetative cell (low penetrance 3)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "94b."
perl -pi -e 's/VIABLE WT cells with some long cells at 25-32/FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002104,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
echo "94c."
perl -pi -e 's/VIABLE WT cells occasionally long at 25-32/FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002104,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies WT cells with some long cells  at 25-32/FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002104,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 95.
# VIABLE slightly long cells at 32, microcolonies long cells at 25 (1)
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance 1 low expressivity 3)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# phenotype population
# FYPO:0002060 viable vegetative cell population
echo "95."
perl -pi -e 's/VIABLE slightly long cells at 32- microcolonies long cells at 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 96.
# VIABLE slightly long cells at 32, small colonies long cells at 25
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance 1 low expressivity 3)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# phenotype population
# FYPO:0002060 viable vegetative cell population
echo "96."
perl -pi -e 's/VIABLE slightly long cells at 32- small colonies long cells at 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 97. 
# VIABLE slightly long cells at 32
# VIABLE small colonies misshapen cells- often long at 25-32- lots of diploids FYPO:0000252 
# VIABLE small colonies long cells- possibly diploidising at 25-32 FYPO:0000252
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance 1 low expressivity 3)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# phenotype population
# FYPO:0002060 viable vegetative cell population
echo "97."
perl -pi -e 's/VIABLE slightly long cells at 32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies misshapen cells- often long at 25-32- lots of diploids/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005| FYPO:0000252,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies long cells- possibly diploidising at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005| FYPO:0000252,PECO:0000005/g' tab_phenotype.csv

# 98. 
# ESSENTIAL microcolonies slightly long cells at 25-32
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/793/
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell, interphase block (high penetrance 1 low expressivity 3)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002061 inviable vegetative cell population 
echo "98."
perl -pi -e 's/ESSENTIAL microcolonies slightly long cells at 25-32/FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 99. 
# VIABLE long cells at 25-32
# VIABLE long slightly misshapen cells at 25-32
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance) (high expressivity??????)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "99."
perl -pi -e 's/VIABLE long cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 100. 
# ESSENTIAL small colonies long cells at 25-32
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell, interphase block (high penetrance 1) 
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# cell population phenotype  
# FYPO:0002061 inviable vegetative cell population
echo "100."
perl -pi -e 's/ESSENTIAL small colonies long cells at 25-32/FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 50.
# VIABLE small colonies stubby cells at 25,32, lots of dead cells
# broad classifier: stubby
# cell phenotype
# FYPO:0002106 viable stubby vegetative cell
# FYPO:0002107 inviable stubby vegetative cell
# cell population phenotype  
# FYPO:0002060 viable vegetative cell population
echo "50."
perl -pi -e 's/VIABLE small colonies stubby cells at 25-32- lots of dead cells/FYPO:0002106,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002107,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 101.
# VIABLE small colonies stubby cells at 25-32
# VIABLE small colonies stubby cells at 25,32 cells grow better at 25
# broad classifier: stubby
# cell phenotype
# FYPO:0002106 stubby viable cell  (high penetrance) 
# population phenotype
# FYPO:0002060 viable vegetative cell population 
echo "101."
perl -pi -e 's/VIABLE small colonies stubby cells at 25-32 cells grow better at 25/FYPO:0002106,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies stubby cells at 25-32/FYPO:0002106,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 102a. 
# VIABLE stubby cells at 25-32- cells not growing at 36
# broad classifier: stubby
# cell phenotype
# FYPO:0002106 stubby viable cell  (high penetrance) 
# *****ADD INVIABLE AT HIGH TEMP
# population phenotype  
# FYPO:0002060 viable vegetative cell population
echo "102a"
perl -pi -e 's/VIABLE stubby cells at 25-32- cells not growing at 36/FYPO:0002106,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 102b. 
# VIABLE stubby cells at 25-32
# broad classifier: stubby
# cell phenotype
# FYPO:0002106 stubby viable cell (high penetrance) 
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "102b"
perl -pi -e 's/VIABLE stubby cells at 25-32/FYPO:0002106,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 102c. 
# VIABLE stubby cells at 25-32
# broad classifier: stubby
# cell phenotype
# FYPO:0002106 stubby viable cell  (high penetrance) 
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "102c"
perl -pi -e 's/VIABLE stubby cells at 25-32/FYPO:0002106,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 103.
# broad classifier: long high penetrance
# VIABLE slightly long cells at 25-32
# VIABLE  slightly long cells at 25-32
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetranhance 1 low expressivity 3)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "103."
perl -pi -e 's/VIABLE slightly long cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
echo "103.b"
perl -pi -e 's/VIABLE  slightly long cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 104. 
# VIABLE long cells at 32   (CARE THIS ISA SUBSTRING, ALL LONGER STRINGS ARE ABOVE)
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance 1 high expressivity )
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "104."
perl -pi -e 's/VIABLE long cells at 32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 105. 
# VIABLE misshapen cells at 25-32
# broad classifier: misshapen viable
# cell phenotype
# FYPO:0001510 viable vegetative cell with abnormal cell shape, normal cell size  
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "105"
perl -pi -e 's/VIABLE misshapen cells at 25-32/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 106.
# VIABLE slightly misshapen cells at 32, VIABLE/ESSENTIAL microcolonies misshapen cells at 25
# VIABLE slightly misshapen cells at 25- VIABLE/ESSENTIAL small colonies slightly misshapen cells at 32
# VIABLE slightly misshapen cells at 32, possibly supressors, lots of dead cells (1)
# VIABLE slightly misshapen cells at 32
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell with abnormal cell shape, normal cell size (low expressivity)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "106."
perl -pi -e 's/VIABLE slightly misshapen cells at 32- VIABLE\/ESSENTIAL microcolonies misshapen cells at 25/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen cells at 25- VIABLE\/ESSENTIAL small colonies slightly misshapen cells at 32/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen cells at 32- possibly supressors- lots of dead cells/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen cells at 32/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 107. 
# VIABLE small colonies slightly long cells at 25-32
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance/low expressivity)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "107"
perl -pi -e 's/VIABLE small colonies slightly long cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 108. 
# VIABLE curved slightly long cells at 32
# VIABLE long curved cells at 25-32- cells longer and misshapen at 36 (removed expressivity)
# broad classifier: curved
# cell phenotype
# FYPO:0002215 viable curved elongated vegetative cell  (high penetrance, low expressivity, checked with Jacky) 843/
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "108a."
perl -pi -e 's/VIABLE curved slightly long cells at 32/FYPO:0002215,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE long curved cells at 25-32- cells longer and misshapen at 36/FYPO:0002215,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 108b . 
# VIABLE small colonies long curved cells at 25-32
# VIABLE curved cells at 32- WT cells at 25- misshapen cells at 36
# broad classifier: curved
# cell phenotype
# FYPO:0002215 viable curved elongated vegetative cell   (high penetrance) 843/
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "108b."
perl -pi -e 's/VIABLE small colonies long curved cells at 25-32/FYPO:0002215,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE curved cells at 32- WT cells at 25- misshapen cells at 36/FYPO:0002215,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 109.
# VIABLE curved slightly long cells at 25-32
# broad classifier: curved
# cell phenotype
# FYPO:0002215 viable curved elongated vegetative cell asked Jacky *******penetrance? expressivity 843/
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "109"
perl -pi -e 's/VIABLE curved slightly long cells at 25-32/FYPO:0002215,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 110a. (asked jacky this should be small, not very small)
# VIABLE very small colonies long cells at 25-32- ESSENTIAL branched cells at 36
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# FYPO:0002461 inviable branched vegetative cell (high  temp)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "110a"
perl -pi -e 's/VIABLE very small colonies long cells at 25-32- ESSENTIAL branched cells at 36/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005| FYPO:0002461,PECO:0000004/g' tab_phenotype.csv

# 110b. (asked jacky this should be small, not very small)
# VIABLE very small colonies long cells at 25,32, possibly suppressors
# VIABLE very small colonies long cells at 25-32
# broad classifier: long high penetrance
# FYPO:0001492 elongated viable vegetative cell (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "110b"
perl -pi -e 's/VIABLE very small colonies long cells at 25-32- possibly suppressors/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies long cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 110c. 
# VIABLE small colonies branched septated cells at 25-32- ESSENTIAL cells long highly branched at 36
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0002459 viable branched, elongated vegetative cell
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# FYPO:0002461 inviable branched vegetative cell (high  temp)
# population phenotype
# FYPO:0002060 viable vegetative cell population
#
echo "110c"
perl -pi -e 's/VIABLE small colonies branched septated cells at 25-32- ESSENTIAL cells long highly branched at 36/FYPO:0002459,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005| FYPO:0002461,PECO:0000004/g' tab_phenotype.csv

# 111. (make sure anything with this in the substring is higher up)
# ESSENTIAL swollen spores at 25-32
# broad classifier: spores (misshapen essential in paper)
# cell phenotype
# FYPO:0002207 inviable swollen spore  (high penetrance) 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "111."
perl -pi -e 's/ESSENTIAL swollen spores at 25-32/FYPO:0002207,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 112.
# VIABLE small colonies rounded cells at 25,32, no growth at 36
# VIABLE small colonies rounded cells at 25-32
# broad classifier: rounded
# cell phenotype
# FYPO:0002380 viable spheroid vegetative cell  (high_penetrance) 
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "112."
perl -pi -e 's/VIABLE small colonies rounded cells at 25-32- no growth at 36/FYPO:0002380,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0002061,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies rounded cells at 25-32/FYPO:0002380,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv




# 113. 
# ESSENTIAL spores- some germinated spores at 25-32 (35)
# broad classifier: spores
# cell phenotype
# FYPO:0000311 inviable after spore germination with normal unseptated germ tube morphology (low penetrance)
# FYPO:0002151 inviable spore (high penetrance)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "113."
perl -pi -e 's/ESSENTIAL spores- some germinated spores at 25-32/FYPO:0000311,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
 
# 114a. 
# ESSENTIAL spores, germinated spores at 25,32 some division
# broad classifier: germination
# cell phenotype 
# FYPO:0000311 inviable after spore germination with normal, unseptated germ tube morphology (high penetrance)
# FYPO:0000312 inviable after spore germination with normal, septated germ tube morphology (low penetrance)
# FYPO:0002151 inviable spore (low penetrance)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "114a."
perl -pi -e 's/ESSENTIAL spores- germinated spores at 25-32 some division/FYPO:0000312,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0000311,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 114b
# ESSENTIAL spores- germinated spores at 25-32 (127)
# ESSENTIAL spores- germinated spores  at 25-32 (2)
# broad classifier: germination
# cell phenotype 
# FYPO:0000311 inviable after spore germination with normal, unseptated germ tube morphology (low penetrance)
# FYPO:0002151 inviable spore (high penetrance)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "114b."
perl -pi -e 's/ESSENTIAL spores- germinated spores at 25-32/FYPO:0002061,PECO:0000005| FYPO:0000311,PECO:0000005| FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000001)/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores  at 25-32/FYPO:0002061,PECO:0000005| FYPO:0000311,PECO:0000005| FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000001)/g' tab_phenotype.csv

# 115.
# ESSENTIAL germinated spores at 25-32 (69)
# broad classifier: germination  
# cell phenotype 
# FYPO:0000311 inviable after spore germination with normal, unseptated germ tube morphology (high penetrance)
# population phenotype
# # FYPO:0002061 inviable vegetative cell population
echo "115."
perl -pi -e 's/ESSENTIAL germinated spores at 25-32/FYPO:0000311,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 116.
# broad classifier: germination
# ESSENTIAL spores- germinated spores- some division at 25-32 (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/837/
# cell phenotype 
# FYPO:0002151 inviable spore (low penetrance)
# FYPO:0000320 inviable after spore germination, single cell division (low penetrance)
# FYPO:0000310 inviable after spore germination with normal germ tube morphology (high penetrate)
# population phenotype
# # FYPO:0002061 inviable vegetative cell population
echo "116."
perl -pi -e 's/ESSENTIAL spores- germinated spores- some division at 25-32/FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0000320,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0000310,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
# asked jacky, not microcolonies, only occasional division

# 117. 
# ESSENTIAL spores- germinated spores- microcolonies skittles cells at 25-32 (2)
# ESSENTIAL spores- germinated spores- microcolonies skittle cells at 25-32
# broad classifier: skittle
# cell phenotype 
# FYPO:0002151 inviable spore 
# FYPO:0000320 inviable skittle cells (high expressivity)
# FYPO:0000310 inviable after spore germination with normal germ tube morphology
# population phenotype
# FYPO:0002061 inviable vegetative cell population 
# penetrance probably split 3 way but not sure so ommitting
echo "117."
perl -pi -e 's/ESSENTIAL spores- germinated spores- microcolonies skittles cells at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000320,PECO:0000005,has_expressivity(FYPO_EXT:0000001)| FYPO:0000310,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores- microcolonies skittle cells at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000320,PECO:0000005,has_expressivity(FYPO_EXT:0000001)| FYPO:0000310,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 118. 
# ESSENTIAL microcolonies skittle cells at 25,32
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell (high penetrance)
# cell population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "118."
perl -pi -e 's/ESSENTIAL microcolonies skittle cells at 25-32/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 119.
# ESSENTIAL microcolonies skittle cells at 32- larger colonies at 25 (1)
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell
# cell population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "119."
perl -pi -e 's/ESSENTIAL microcolonies skittle cells at 32- larger colonies at 25/FYPO:0002111,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 120.a
# ESSENTIAL microcolonies skittle cells at 32- small colonies skittle cells at 25 (1)
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell (high penetrance?)
# cell population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "120.a"
perl -pi -e 's/ESSENTIAL microcolonies skittle cells at 32- small colonies skittle cells at 25/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 120.b
# ESSENTIAL microcolonies skittle slightly misshapen cells at 25-32 (5)
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell
# cell population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "120.b"
perl -pi -e 's/ESSENTIAL microcolonies skittle slightly misshapen cells at 25-32/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 121.
# ESSENTIAL microcolonies slightly skittle cells at 25-32 (1)
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell (expressivity low)
# cell population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "121."
perl -pi -e 's/ESSENTIAL microcolonies slightly skittle cells at 25-32/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 122.
# ESSENTIAL microcolonies small cells- often skittle at 25-32 (1) CHECK UP ON THIS (**********JACKY checking)

# 123. DUPLICATE OF 117
# ESSENTIAL spores- germinated spores- microcolonies skittle cells at 25-32 (1)
echo "no 123."

# 124.
# ESSENTIAL spores  at 32- microcolonies skittle cells at 25 (1) (**********JACKY checking)

# 125. 
# ESSENTIAL microcolonies rounded skittle cells at 25-32 (1)
# broad classifier: skittle
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell 
# cell population phenotype
# FYPO:0002061 inviable vegetative cell population 
echo "125."
perl -pi -e 's/ESSENTIAL microcolonies rounded skittle cells at 25-32/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 126.
# ESSENTIAL microcolonies skittle- rounded cells at 25-32 (6)
# broad classifier: skittle
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell
# cell population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "126"
perl -pi -e 's/ESSENTIAL microcolonies skittle- rounded cells at 25-32/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 127.
# ESSENTIAL microcolonies skittle cells 32- cells more rounded at 25 (1)
# broad classifier: skittle
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/808/
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell 
# cell population phenotype 
# FYPO:0002061 inviable vegetative cell population
echo "127."
perl -pi -e 's/ESSENTIAL microcolonies skittle cells 32- cells more rounded at 25/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 128.
# ESSENTIAL microcolonies skittle cells at 32- cells more rounded at 25 (1)
# broad classifier: skittle
# cell phenotype
# FYPO:0002111 bottle-shaped inviable vegetative cell 
# cell population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "128."
perl -pi -e 's/ESSENTIAL microcolonies skittle cells at 32- cells more rounded at 25/FYPO:0002111,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 129
# ESSENTIAL germinated spores- microcolonies rounded skittle cells at 25-32 (1)
# broad classifier: skittle
# cell phenotype 
# FYPO:0000320 inviable skittle cells (penetrance??????********)
# FYPO:0000310 inviable after spore germination with normal germ tube morphology (penetrance????********)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo  "129."
perl -pi -e 's/ESSENTIAL germinated spores- microcolonies rounded skittle cells at 25-32/FYPO:0000320,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0002061,PECO:0000005/g'  tab_phenotype.csv


# 130.  
# ESSENTIAL small colonies rounded cells at 25,32, lysis after 48h  PLUS  FYPO:0000647 cell lysis (1)
# ESSENTIAL small colonies rounded cells at 25,32 (1)
# ESSENTIAL small colonies rounded cells at 32, cells longer at 25 (1)
# ESSENTIAL small colonies rounded cells at 32, larger colonies at 25 (1)
# broad classification: rounded
# cell phenotype
# FYPO:0002187 inviable normal volume spheroid vegetative cell  (SF 780) (HIGH PENETRANT)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "130 a."
perl -pi -e 's/ESSENTIAL small colonies rounded cells at 25-32- lysis after 48h/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|FYPO:0000647,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "130 b."
perl -pi -e 's/ESSENTIAL small colonies rounded cells at 25-32/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "130 c."
perl -pi -e 's/ESSENTIAL small colonies rounded cells at 32- cells longer at 25/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "130 d."
perl -pi -e 's/ESSENTIAL small colonies rounded cells at 32- larger colonies at 25/FYPO:0002187,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 131. 
# ESSENTIAL microcolonies rounded septated cells at 25-32 (1)
# broad classification: rounded
# cellular phenotype
# FYPO:0002193 inviable normal volume septated spheroid vegetative cell (806)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "131."
perl -pi -e 's/ESSENTIAL microcolonies rounded septated cells at 25-32/FYPO:0002193,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 132.
# ESSENTIAL microcolonies large rounded septated cells at 25-32 (1)
# broad classification: rounded
# cellular phenotype
# FYPO:0002240 swollen septated spheroid vegetative cell (806)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "132"
perl -pi -e 's/ESSENTIAL microcolonies large rounded septated cells at 25-32/FYPO:0002240,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 133. 
# LONG SKITTLE (weak)
# broad classification: long high penetrance
# ESSENTIAL microcolonies long- weak skittle cells at 25-32 (1)
# ESSENTIAL microcolonies long slight skittle cells at 25-32 (1)
# cellular phenotype
# # FYPO:0002242 inviable elongated bottle-shaped vegetative cell (high penetrance, low expressivity)
# # FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "133."
perl -pi -e 's/ESSENTIAL microcolonies long- weak skittle cells at 25-32/FYPO:0002242,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g'  tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies long slight skittle cells at 25-32/FYPO:0002242,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g'  tab_phenotype.csv

# 134. 
#  ESSENTIAL microcolonies stubby cells at 25-32 (1) 
#  ESSENTIAL microcolonies stubby cells at 25- cells slightly misshapen at 32 (1)
#  ESSENTIAL microcolonies stubby cells at 25-32 (1)
#  ESSENTIAL microcolonies stubby cells at 32 cells more misshapen at 25 (1)
#  broad classification: stubby
#  cell phenotype
#  FYPO:0002107 stubby inviable cell (high penetrance)
#  population phenotype
#  FYPO:0002061 inviable vegetative cell population
echo "134.a"
perl -pi -e 's/ESSENTIAL microcolonies stubby cells at 25-32/FYPO:0002107,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "134.b"
perl -pi -e 's/ESSENTIAL microcolonies stubby cells at 25- cells slightly misshapen at 32/FYPO:0002107,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "134.c"
perl -pi -e 's/ESSENTIAL microcolonies stubby cells at 25-32/FYPO:0002107,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "134.d"
perl -pi -e 's/ESSENTIAL microcolonies stubby cells at 32 cells more misshapen at 25/FYPO:0002107,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 135. ignore long
# broad classification: stubby
# ESSENTIAL microcolonies stubby cells- occasionally long at 25-32 (1)
# cell phenotype
# FYPO:0002107 stubby inviable cell
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "135."
perl -pi -e 's/ESSENTIAL microcolonies stubby cells- occasionally long at 25-32/FYPO:0002107,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 136.
# broad classifier: stubby
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/801/
# ESSENTIAL microcolonies stubby- septated cells at 25-32 (1) (high penetrance)
# ESSENTIAL microcolonies stubby- septated cells- some lysis at 25-32 (1) (high penetrance)
# cell phenotype
# ntr: inviable stubby septated cells
# FYPO:0002200 inviable stubby septated vegetative cell (801)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
#####add lysis ************
echo "136.a"
perl -pi -e 's/ESSENTIAL microcolonies stubby- septated cells at 25-32/FYPO:0002200,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "136.b"
perl -pi -e 's/ESSENTIAL microcolonies stubby- septated cells- some lysis at 25-32/FYPO:0002200,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 137. Asked Jacky if these really are small colonies (yes recheck numbes)
# ESSENTIAL small colonies stubby cells at 25-32 (1)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/801/
# broad classifier: stubby
# cell phenotype
# FYPO:0002107 stubby inviable cell (high penetrance ????)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "137."
perl -pi -e 's/ESSENTIAL small colonies stubby cells at 25-32/FYPO:0002107,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 138.
# broad classifier: long high penetrance
# ESSENTIAL germinated spores long curved at 25-32 (1)
# ESSENTIAL germinated spores- often long and curved at 25-32 (1)
# cell phenotype
# FYPO:0002212 inviable after spore germination with elongated, curved germ tube (high penetrance) (843)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "138.a"
perl -pi -e 's/ESSENTIAL germinated spores long curved at 25-32/FYPO:0002212,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "138.b"
perl -pi -e 's/ESSENTIAL germinated spores- often long and curved at 25-32/FYPO:0002212,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 139.  ASKED JACKY ************
# broad classifier: long high penetrance
# ESSENTIAL germinated spores long curved- often divide at 25-32 (1)
# cellular phenotype
# FYPO:0002212  inviable after spore germination, with curved elongated germ tube (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# FYPO:0002279 inviable after spore germination, single cell division, with elongated, curved germ tube 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "139."
perl -pi -e 's/ESSENTIAL germinated spores long curved- often divide at 25-32/FYPO:0002212,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|FYPO:0002279,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv


# 140.  need to decide how to represent (ask jacky) (cant annotate expressivity)
# long high penetrance (with curved)
# ESSENTIAL microcolonies long cells- often curved at 25-32 (1)
# ESSENTIAL microcolonies long curved cells at 25-32 (4)
# ESSENTIAL microcolonies long curved misshapen cells at 32- microcolonies with some long cells at 25 (1)
# ESSENTIAL microcolonies long slightly curved cells at 25-32 (1)
# ESSENTIAL microcolonies long slightly curved cells- colonies appear dark at 25-32 (1)
# cell phenotype
# FYPO:0000059 abnormal mitotic cell cycle progression
# FYPO:0002411 Inviable curved elongated vegetative cell
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo 140 a.
perl -pi -e 's/ESSENTIAL microcolonies long cells- often curved at 25-32/FYPO:0002411,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo 140 b.
perl -pi -e 's/ESSENTIAL microcolonies long curved cells at 25-32/FYPO:0002411,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo 140 c.
perl -pi -e 's/ESSENTIAL microcolonies long curved misshapen cells at 32- microcolonies with some long cells at 25/FYPO:0002411,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo 140 d.
perl -pi -e 's/ESSENTIAL microcolonies long slightly curved cells at 25-32/FYPO:0002411,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo 140 e.
perl -pi -e 's/ESSENTIAL microcolonies long slightly curved cells- colonies appear dark at 25-32/FYPO:0002411,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000741,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 141. 
# ESSENTIAL microcolonies slightly long curved cells at 25-32 (1)
# broad classifier curved
# cell phenotype
# difficult because low expressivity only applied to long
# FYPO:0002113 inviable curved vegetative cell
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "141."
perl -pi -e 's/ESSENTIAL microcolonies slightly long curved cells at 25-32/FYPO:0002113,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

echo "142"

# 143.
#  broad classifier: curved
#  ESSENTIAL microcolonies curved septated cells at 25- 32  (1) 
#  ESSENTIAL microcolonies curved septated cells at 25-32 (2) 
#  cell phenotype
#  FYPO:0002282 curved inviable septated cell (851) (high penetrance)
#  population phenotype
#  FYPO:0002061 inviable vegetative cell population
echo "143.a"
perl -pi -e 's/ESSENTIAL microcolonies curved septated cells at 25- 32/FYPO:0002282,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "143.b"
perl -pi -e 's/ESSENTIAL microcolonies curved septated cells at 25-32/FYPO:0002282,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 144.
# a. ESSENTIAL microcolonies curved cells at 32- cells more WT at 25 (1)
# b. ESSENTIAL microcolonies slightly misshapen curved cells  at 25-32 (1) 
# c. ESSENTIAL microcolonies slightly misshapen curved cells  at 25-32
# d ESSENTIAL microcolonies misshapen curved cells at 25-32 (high penetrance
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/814/
# cell phenotype
# FYPO:0002113 curved inviable cell (high penetrance?)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
# echo 144.a.
perl -pi -e 's/ESSENTIAL microcolonies curved cells at 32- cells more WT at 25/FYPO:0002113,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
# echo 144.b.
perl -pi -e 's/ESSENTIAL microcolonies curved cells at 32- cells more WT at 25/FYPO:0002113,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
# echo 144.c.
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen curved cells  at 25-32/FYPO:0002113,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
# echo 144.d.
perl -pi -e 's/ESSENTIAL microcolonies misshapen curved cells at 25-32/FYPO:0002113,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 145.
# ESSENTIAL microcolonies curved misshapen cells- colonies have a dark edge at 25-32 (1)
# broad classifier: curved
# cell phenotype
# FYPO:0002113 curved inviable cell
# FYPO:0000741 increased  cellular pigment accumulation
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "145."
perl -pi -e 's/ESSENTIAL microcolonies curved misshapen cells- colonies have a dark edge at 25-32/FYPO:0002113,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0000741,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 146.
# ESSENTIAL microcolonies curved misshapen swollen cells at 25-32  (1)
# broad classifier: curved
# cell phenotype
# FYPO:0002230 inviable swollen curved vegetative cell  (high penetrance?) 
# population phenotype 
# FYPO:0002061 inviable vegetative cell population
echo "146."
perl -pi -e 's/ESSENTIAL microcolonies curved misshapen swollen cells at 25-32/FYPO:0002230,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

echo "147."

# 148.
# ESSENTIAL microcolonies slightly curved vacuolated cells at 25-32 (1)
# broad classifier: curved
# cell phenotype
# FYPO:0002250: inviable curved vacuolated vegetative cell (LOW expressivity) 
# population phenotype 
# FYPO:0002061 inviable vegetative cell population
echo "148."
perl -pi -e 's/ESSENTIAL microcolonies slightly curved vacuolated cells at 25-32/FYPO:0002250,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 149.
# VIABLE small colonies long curved cells at 32- ESSENTIAL microcolonies long cells at 25-36 (1)
# broad phenotype: long high penetrance
# cell phenotype
# FYPO:0002215 elongated curved viable vegetative cell (standard temp)  
# FYPO:0001490 elongated inviable vegetative cell  (high temp/ low temperature) 
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population  phenotypes
# FYPO:0002217 viable curved elongated vegetative cell population ÉÉÉsmall colonies viable elongated curved (standard temp) (854/855) 
# FYPO:0002061 inviable vegetative cell population
echo "149."
perl -pi -e 's/VIABLE small colonies long curved cells at 32- ESSENTIAL microcolonies long cells at 25-36/FYPO:0002215,PECO:0000005| FYPO:0001490,PECO:0000004| FYPO:0001490,PECO:0000006| FYPO:0002060,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000004| FYPO:0002061,PECO:0000006/g' tab_phenotype.csv

# 151
# ESSENTIAL microcolonies slightly small cells at 25-32
# small
# cell phenotype
# FYPO:0000951 small inviable vegetative cell high penetrance, low expressivity
# population  phenotypes
# FYPO:0002061 inviable vegetative cell population 
echo "151."
perl -pi -e 's/ESSENTIAL microcolonies slightly small cells at 25-32/FYPO:0000951,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 152
# ESSENTIAL spores- some germinated spores long at 25-32  (this was originally annotated as "spores")
# ESSENTIAL spores- germinated spores- occasionally long at 25-32
# ESSENTIAL spores- germinated spores- some long at 25-32
# broad classifier: long low penetrance 
# cell phenotype
# FYPO:0000314 inviable after spore germination with elongated germ tube (low pen)
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology 
# FYPO:0002151 inviable spore (high pen)
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "152."
perl -pi -e 's/ESSENTIAL spores- some germinated spores long at 25-32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores- occasionally long at 25-32-/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores- occasionally long at 25-32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059/g' tab_phenotype.csv

perl -pi -e 's/ESSENTIAL spores- germinated spores- some long at 25-32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059/g' tab_phenotype.csv

# 153
# a) ESSENTIAL germinated spores long at 25- germinated spores slightly long at 32  (1) (expressivity low)
# b) ESSENTIAL germinated spores slightly long at 25-32 (2) (expressivity low)
# c) ESSENTIAL germinated spores long misshapen at 25-32 (2)
# d) ESSENTIAL germinated spores long often misshapen at 25-32 (1)
# e) ESSENTIAL germinated spores long at 32- spores and germinated spores at 25
# long high penetrance
# cell phenotype
# FYPO:0002379 inviable after spore germination, without cell division, with elongated germ tube
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002061 inviable vegetative cell population

echo "153a"
perl -pi -e 's/ESSENTIAL germinated spores long at 25- germinated spores slightly long at 32/FYPO:0002379,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "153b"
perl -pi -e 's/ESSENTIAL germinated spores slightly long at 25-32/FYPO:0002379,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "153c"
perl -pi -e 's/ESSENTIAL germinated spores long misshapen at 25-32/FYPO:0002379,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "153d"
perl -pi -e 's/ESSENTIAL germinated spores long often misshapen at 25-32/FYPO:0002379,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores long at 32- spores and germinated spores at 25/FYPO:0002379,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005| FYPO:0002061,PECO:0000006| FYPO:0001991,PECO:0000006/g' tab_phenotype.csv

# 154
# ESSENTIAL germinated spores long- lysis at 25-32  (6) 
# ESSENTIAL germinated spores long misshapen- lysis at 25-32 (1) 
# broad qualifier: long high penetrance
# cell phenotype
# FYPO:0002379 inviable after spore germination without cell division with  elongated germ tube (expressivity low) (penetrance high)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# FYPO:0002294 lysed cell after spore germination with elongated germ tube  (expressivity low) (penetrance low) 
# population phenotype 
# FYPO:0002061 inviable vegetative cell population
echo "154a"
perl -pi -e 's/ESSENTIAL germinated spores long- lysis at 25-32/FYPO:0000314,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002294,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000003) | FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "154b"
perl -pi -e 's/ESSENTIAL germinated spores long misshapen- lysis at 25-32/FYPO:0000314,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002294,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 155.
# long high penetrance
# ESSENTIAL germinated spores long- some microcolonies long cells at 25-32 (1)
# ESSENTIAL germinated spores long- microcolonies long cells at 25-32 (4)
# ESSENTIAL germinated spores long- microcolonies with some long cells at 25-32 (5)
# ESSENTIAL germinated spores long- some division at 32- microcolonies long cells at 25 (1)
# cell phenotype
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell, interphase block 
# FYPO:0000314 inviable after spore germination with elongated germ tube (high pentrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "155a"
perl -pi -e 's/ESSENTIAL germinated spores long- some microcolonies long cells at 25-32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0003529,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "155b"
perl -pi -e 's/ESSENTIAL germinated spores long- microcolonies long cells at 25-32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0003529,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "155c"
perl -pi -e 's/ESSENTIAL germinated spores long- microcolonies with some long cells at 25-32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0003529,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "155d"
perl -pi -e 's/ESSENTIAL germinated spores long- some division at 32- microcolonies long cells at 25/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0003529,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv


# 156
# similar to 155
# long high penetrance
# ESSENTIAL germinated spores long- some division at 25- microcolonies with some long cells at 32
# ESSENTIAL germinated spores long at 32- microcolonies long cells at 25
# cell phenotype
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell, interphase block 
# FYPO:0000314 inviable after spore germination with elongated germ tube (high pentrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "156."
perl -pi -e 's/ESSENTIAL germinated spores long- some division at 25- microcolonies with some long cells at 32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0003529,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores long at 32- microcolonies long cells at 25/FYPO:0000314,PECO:0000005| FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 157
echo "157."

# 158  
# broad classifier: long high penetrance
# i) ESSENTIAL germinated spores long at 25-32- often divide at 32 (2) (I have ignored the dividing at 32, because it doesn't fit our temperature split well, might fix later)
# a) 1 ESSENTIAL germinated spores long often divide at 25-32
# b) 1 ESSENTIAL germinated spores long at 32- more division at 25
# c) 2 ESSENTIAL germinated spores long- often divide 25-32
# d) 2 ESSENTIAL germinated spores long- often divide at 25-32
# e) 1 ESSENTIAL germinated spores long- often divide once at 25-32
# f) 8 ESSENTIAL germinated spores long- some division at 25-32
# g) 1 ESSENTIAL germinated spores long- occasionally divide 25-32
# h) 1 ESSENTIAL germinated spores long- occasionally divide at 25-32
# cell phenotypes
# FYPO:0000314 inviable after spore germination with elongated germ tube
# FYPO:0001042 inviable after spore germination, single or double cell division
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "158a"
perl -pi -e 's/ESSENTIAL germinated spores long at 25-32- often divide at 32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores long often divide at 25-32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "158b"
perl -pi -e 's/ESSENTIAL germinated spores long at 32- more division at 25/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "158c"
perl -pi -e 's/ESSENTIAL germinated spores long- often divide 25-32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "158d"
perl -pi -e 's/ESSENTIAL germinated spores long- often divide at 25-32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "158e"
perl -pi -e 's/ESSENTIAL germinated spores long- often divide once at 25-32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "158f"
perl -pi -e 's/ESSENTIAL germinated spores long- some division at 25-32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "158g"
perl -pi -e 's/ESSENTIAL germinated spores long- occasionally divide 25-32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "158h"
perl -pi -e 's/ESSENTIAL germinated spores long- occasionally divide at 25-32/FYPO:0000314,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "158i"

# 159.
# broad classifier: long high penetrance  
# ESSENTIAL germinated spores long at 25-32 (51)
# cell phenotype
# FYPO:0000314 inviable after spore germination with elongated germ tube (HIGH PENTRANCE)  
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "159."
perl -pi -e 's/ESSENTIAL germinated spores long at 25-32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv


# 160a.
# long low penetrance
# ESSENTIAL germinated spores at 25- germinated spores- occasionally long at 32
# ESSENTIAL germinated spores- occasionally long at 25-32
# ESSENTIAL germinated spores- occasionally long at 32 not so long at 25 (was called long high pen in spreadsheet, should be low)
# cell phenotype
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology (high pen)
# FYPO:0002379 inviable after spore germination, without cell division, with elongated germ tube (low pen)
# FYPO:0000059 abnormal mitotic cell cycle progression  (low pen)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "160a."
perl -pi -e 's/ESSENTIAL germinated spores at 25- germinated spores- occasionally long at 32/FYPO:0000310,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002379,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores- occasionally long at 25-32/FYPO:0000310,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002379,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores- occasionally long at 32 not so long at 25/FYPO:0000310,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002379,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
 
# 160b.
# long low penetrance
# 1 ESSENTIAL germinated spores- occasionally long- occasionally divide at 25-32
# 1 ESSENTIAL germinated spores- occasionally long- some division at 25-32 
# cell phenotype
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology (high pen)
# FYPO:0002379 inviable after spore germination, without cell division, with elongated germ tube (low pen)
# FYPO:0002280 inviable after spore germination, single cell division
# FYPO:0000059 abnormal mitotic cell cycle progression  (low pen)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "160b."
perl -pi -e 's/ESSENTIAL germinated spores- occasionally long- occasionally divide at 25-32/FYPO:0000310,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002379,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002280,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores- occasionally long- some division at 25-32/FYPO:0000310,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002379,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002280,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 161
echo "161."

# 162a.
# 
# broad classifier: misshapen essential
# ESSENTIAL germinated spores misshapen- microcolonies misshapen cells at 25-32
# ESSENTIAL misshapen germinated spores- microcolonies misshapen cells at 25-32
# ESSENTIAL misshapen germinated spores and microcolonies misshapen cells at 32
# ESSENTIAL misshapen germinated spores- microcolonies misshapen septated cells at 25-32
# cell phenotype
# FYPO:0000313 inviable after spore germination, without cell division, with abnormal germ tube morphology
# FYPO:0002429 inviable germinated spore, multiple cell divisions, abnormal shape (normal size)  
# population phenotype
# FYPO:0002061 inviable vegetative cell population
# 
echo "162a."
perl -pi -e 's/ESSENTIAL germinated spores misshapen- microcolonies misshapen cells at 25-32/FYPO:0000313,PECO:0000005| FYPO:0002429,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL misshapen germinated spores- microcolonies misshapen cells at 25-32/FYPO:0000313,PECO:0000005| FYPO:0002429,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL misshapen germinated spores and microcolonies misshapen cells at 32/FYPO:0000313,PECO:0000005| FYPO:0002429,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL misshapen germinated spores- microcolonies misshapen septated cells at 25-32/FYPO:0000313,PECO:0000005| FYPO:0002429,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 162b.
# misshapen essential
# ESSENTIAL germinated spores misshapen at 25-32 (18) (non dividing) 
# cell phenotype
# FYPO:0000313 inviable after spore germination, without cell division, with abnormal germ tube morphology (high_penetrance)
# population phenotype 
# FYPO:0002061 inviable vegetative cell population
echo "162b."
perl -pi -e 's/ESSENTIAL germinated spores misshapen at 25-32/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 163
# misshapen essential
# DIVIDE OCCASIONALLY or some division = divides once or twice
# a) 1 ESSENTIAL germinated spores slightly misshapen- occasionally divide at 25-32
# b) 12 ESSENTIAL germinated spores slightly misshapen- some division at 25-32
# c) 2 ESSENTIAL germinated spores misshapen- some division at 25-32
# d) 1 ESSENTIAL germinated spores slightly misshapen and divide once at 25-32
# e) 24 ESSENTIAL germinated spores slightly misshapen and divide once at 25-32
# f) 1 ESSENTIAL germinated spores slightly misshapen and divide once at 32- microcolonies misshapen cells at 25
# g) 2 ESSENTIAL germinated spores slightly misshapen- divide once at 25-32
# h) 5 ESSENTIAL germinated spores slightly misshapen- often divide once at 25-32
# i) 1 ESSENTIAL germinated spores slightly misshapen- often divide at 25-32
# j) ESSENTIAL germinated spores slightly misshapen- occasionally long then divide at 25-32 (*** add annotation fo occasionally long)
# cell phenotype
# FYPO:0000313 inviable after spore germination, abnormal germ tube morphology has_penetrance(HIGH
# FYPO:0001042 inviable after spore germination, single or double cell division has_penetrance(LOW
# population phenotype 
# FYPO:0002061 inviable vegetative cell population

echo  "163 a"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen- occasionally divide at 25-32/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001042,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "163 b"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen- some division at 25-32/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001042,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "163 c"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen and divide once at 25-32/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001042,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "163 d"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen and divide once at 25-32/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001042,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "163 e"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen and divide once at 25-32/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001042,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "163 f"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen and divide once at 32- microcolonies misshapen cells at 25/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001042,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "163 g"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen- divide once at 25-32/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001042,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "163 h"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen- often divide once at 25-32/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001042,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "163 i"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen- often divide at 25-32/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001042,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "163 j"
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen- occasionally long then divide at 25-32/FYPO:0000313,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001042,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 164.
# VIABLE slightly misshapen cells at 25,32, cells long septated misshapen at 36 (1)
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 viable elongated vegetative cell  (high temp) (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (high temperature)
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (standard temp) (low expressivity)
# population phenotype
# FYPO:0002060 viable vegetative cell population (high temp)
# FYPO:0002060 viable vegetative cell population (standard_temp) 

echo "164."
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32- cells long septated misshapen at 36/FYPO:0001492,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000004| FYPO:0002060,PECO:0000004| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 165.
# VIABLE slightly misshapen cells at 25,32, cells more misshapen after several divisions (1)
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (low expressivity) (high penetrance)
# population phenotype
# FYPO:0002060 viable vegetative cell population

echo "165."
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32- cells more misshapen after several divisions/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv


# 166.
# VIABLE slightly misshapen cells at 25,32, cells more misshapen, occasionally slightly curved at 36 (1)
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (low expressivity) (high penetrance) (normal temp)
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (low expressivity) (high penetrance) (high temp)
# FYPO:0002112 viable curved vegetative cell  (low expressivity) (low penetrance) (high temp)
# population phenotype
# FYPO:0002060 viable vegetative cell population (normal temp)

echo "166."
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32- cells more misshapen- occasionally slightly curved at 36/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0001510,PECO:0000004,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002112,PECO:0000004,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 166b
# VIABLE slightly misshapen cells at 25,32, ESSENTIAL long misshapen cells at 36
# VIABLE slightly misshapen cells at 25,32, ESSENTIAL microcolonies misshapen cells at 36.
# broad classifier : misshapen viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (standard temp) (high penetrance)
# FYPO:0001490 inviable elongated vegetative cell (high temp) (high penetrance)
# FYPO:0002451 inviable vegetative cell with abnormal cell shape (high temp) (high penetrance)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "166b."
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32- ESSENTIAL long misshapen cells at 36/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0001490,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32- ESSENTIAL microcolonies misshapen cells at 36./FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002451,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 167.
# VIABLE slightly misshapen cells at 25,32
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  (low expressivity) (high penetrance)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population 
echo "167."
perl -pi -e 's/VIABLE slightly misshapen cells at 25-32/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 168. 
# ESSENTIAL germinated spores- some long at 25-32
# broad classifier: long low penetrance
# cell phenotype
# FYPO:0000059 abnormal mitotic cell cycle progression 
# FYPO:0002379 inviable after spore germination, no cell division, with elongated germ tube
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# population phenotype
# FYPO:0002061 inviable vegetative cell population (standard temp)
echo "168a"
perl -pi -e 's/ESSENTIAL germinated spores- some long at 25-32/FYPO:0000059,PECO:0000005| FYPO:0002379,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0000310,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 168b
# VIABLE small colonies slightly misshapen cells at 25- ESSENTIAL microcolonies misshapen cells at 32/
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology  (standard temp)
# FYPO:0002148 inviable after spore germination, multiple cell divisions, abnormal morphology (high temperature)
# population phenotype 
# FYPO:0002061 inviable vegetative cell population (high temperature)
# FYPO:0002060 viable vegetative cell population (standard temp)
# echo "168b."
perl -pi -e 's/VIABLE small colonies slightly misshapen cells at 25- ESSENTIAL microcolonies misshapen cells at 32/FYPO:0002177,PECO:0000004| FYPO:0002148,PECO:0000005| FYPO:0002060,PECO:0000005|  FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 169.
# broad classifier misshapen essential
# ESSENTIAL microcolonies misshapen cells 32
# ESSENTIAL microcolonies misshapen cells at 32- germinated spores at 25
# ESSENTIAL microcolonies misshapen cells at 32
# ESSENTIAL microcolonies misshapen cells- lysis at 25-32 ( add lysis)
# ESSENTIAL microcolonies slightly misshapen cells- lysis at 25-32 ( add lysis) (add low expressivity)
# ESSENTIAL microcolonies misshapen cells at 32- slightlylarger colonies misshapen cells at 25
# ESSENTIAL microcolonies slightly misshapen septated cells at 25-32
# ESSENTIAL microcolonies misshapen cells at 25 longer cells at 32
# ESSENTIAL small colonies misshapen septated cells at 25-32
# ESSENTIAL misshapen spores- microcolonies misshapen cells 25- 32 ( add spores)
# ESSENTIAL microcolonies slightly misshapen cells- colonies dark in colour at 32- spores at 25 (add low expressivity) (add altered colour FYPO:0000741)
# cell phenotype
# FYPO:0002148 inviable after spore germination, multiple cell divisions, abnormal morphology (high_penetrance)
# population phenotype 
# FYPO:0002061 inviable vegetative cell population


echo "169a"
perl -pi -e 's/ESSENTIAL microcolonies misshapen cells at 32- germinated spores at 25/FYPO:0002148,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies misshapen cells at 32- slightlylarger colonies misshapen cells at 25/FYPO:0002148,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005| FYPO:0000647,PECO:0000005/g' tab_phenotype.csv
echo "169b."
perl -pi -e 's/ESSENTIAL microcolonies misshapen cells at 32/FYPO:0002148,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "169c"
perl -pi -e 's/ESSENTIAL microcolonies misshapen cells- lysis at 25-32/FYPO:0002148,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000647,PECO:0000005/g' tab_phenotype.csv
echo "169d"
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells- lysis at 25-32/FYPO:0002148,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005| FYPO:0000647,PECO:0000005/g' tab_phenotype.csv
echo "169e."
perl -pi -e 's/ESSENTIAL microcolonies misshapen cells 32/FYPO:0002148,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen septated cells at 25-32/FYPO:0002148,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies misshapen cells at 25 longer cells at 32/FYPO:0002148,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL small colonies misshapen septated cells at 25-32/FYPO:0002148,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL misshapen spores- microcolonies misshapen cells 25- 32/FYPO:0002148,PECO:0000005| FYPO:0002427,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells- colonies dark in colour at 32- spores at 25/FYPO:0002148,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002427,PECO:0000005| FYPO:0002061,PECO:0000005| FYPO:0000741,PECO:0000005/g' tab_phenotype.csv


# 170.
# VIABLE slightly curved- stubby septated cells at 25,32, cells misshapen at 36 (ignored high temp)
# broad classifier: stubby
# cell phenotype
# FYPO:0002406 viable curved stubby septated vegetative cell
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population
echo "170."
perl -pi -e 's/VIABLE slightly curved- stubby septated cells at 25-32- cells misshapen at 36/FYPO:0002406,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 171.
# ESSENTIAL germinated spores, occasionally long and then divide at 25, 32
# broad classifier : long low pen (was germination)
# cell phenotype
# FYPO:0000310 inviable after spore germination with normal germ tube morphology (high penetrance)
# FYPO:0002409 inviable after spore germination, single cell division, with elongated germ tube
# cell population
# FYPO:0002061 inviable vegetative cell population
echo "171."
perl -pi -e 's/ESSENTIAL germinated spores- occasionally long and then divide at 25- 32/FYPO:0000310,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002409,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 172.
echo "172"

# 173
# VIABLE very small colonies WT cells at 25,32
# VIABLE small colonies WT cells at 32, cells slightly misshapen at 25
# VIABLE WT cells at 25- 32
# VIABLE small colonies WT cells at 32, cells WT at 25, very small colonies at 36
# VIABLE small colonies WT cells at 32
# broad classifier: WT
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology  (high penetrance)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "173." 
perl -pi -e 's/VIABLE small colonies WT cells at 32- cells slightly misshapen at 25/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies WT cells at 25-32/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE WT cells at 25- 32/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies WT cells at 32- cells WT at 25- very small colonies at 36/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies WT cells at 32/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 174
# ESSENTIAL microcolonies slightly misshapen vacuolated cells at 25-32
# broad classifier: essential misshapen
# cell phenotype
# FYPO:0002410 inviable vegetative misshapen vacuolated cell  (high_penetrance/ low expressivity) 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "174."
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen vacuolated cells at 25-32/FYPO:0002410,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 175. (not annotated longer at 36)
# VIABLE very small colonies slightly misshapen cells at 25-32- cells longer at 36
# VIABLE very small colonies slightly misshapen cells at 25-32
# broad classifier: misshapen weak viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (low expressivity) (high penetrance)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population
echo  "175a."
perl -pi -e 's/VIABLE very small colonies slightly misshapen cells at 25-32- cells longer at 36/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
echo  "175b."
perl -pi -e 's/VIABLE very small colonies slightly misshapen cells at 25-32/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 176
# ESSENTIAL microcolonies swollen- misshapen cells at 25-32
# cell phenotype
# FYPO:0002415 inviable swollen misshapen cell 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo  "176."
perl -pi -e 's/ESSENTIAL microcolonies swollen- misshapen cells at 25-32/FYPO:0002415,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 177   ****EXPRESSIVITY IS WRONG HERE&lt; OCCASIONALLY CURVED
# VIABLE small colonies slightly curved- slightly curved cells at 25-32
# VIABLE small colonies WT cells- occasionally curved at 25-32
# VIABLE small colonies WT cells- occasionally curved  at 25-32
# VIABLE small colonies WT cells- some curved at 25-32
# VIABLE curved cells at 32- WT cells at 25- misshapen cells at 36
# VIABLE  slightly curved slightly misshapen cells at 25-32-  cells dead at 36 (add inviable at high temperature)
# cell phenotype
# FYPO:0002112 curved viable cell  (standard) high penetrance?) low expressivity
# FYPO:0002177 viable vegetative cell with normal cell morphology
# population phenotype
# FYPO:0002060 viable vegetative cell  population (standard temp)
echo "177."
perl -pi -e 's/VIABLE small colonies slightly curved- slightly curved cells at 25-32/FYPO:0002112,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)|  FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies WT cells- occasionally curved at 25-32/FYPO:0002112,PECO:0000005,has_penetrance(FYPO_EXT:0000003),has_expressivity(FYPO_EXT:0000003)| FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies WT cells- occasionally curved  at 25-32/FYPO:0002112,PECO:0000005,has_penetrance(FYPO_EXT:0000003),has_expressivity(FYPO_EXT:0000003)| FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies WT cells- some curved at 25-32/FYPO:0002112,PECO:0000005,has_penetrance(FYPO_EXT:0000003),has_expressivity(FYPO_EXT:0000003)| FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE curved cells at 32- WT cells at 25- misshapen cells at 36/FYPO:0002112,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE  slightly curved slightly misshapen cells at 25-32-  cells dead at 36/FYPO:0002112,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005| FYPO:0002061,PECO:0000004/g' tab_phenotype.csv

# 178a.
# ESSENTIAL spores- germinated spores long- often very long- occasionally microcolonies with some long cells at 25-32
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0002151 inviable spore
# FYPO:0000314 inviable after spore germination with elongated germ tube 
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell, interphase block (low pen)
# FYPO:0000059 abnormal mitotic cell cycle progression
# population phenotype
# FYPO:0002061 inviable vegetative cell population
# echo "178."
perl -pi -e 's/ESSENTIAL spores- germinated spores long- often very long- occasionally microcolonies with some long cells at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000314,PECO:0000005| FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005| FYPO:0000059/g' tab_phenotype.csv

# 178b (as above but germ tube not elongated ??)
# e) ESSENTIAL spores- germinated spores- small colonies long cells at 25-32
# broad classifier: long high penetrance
# cell phenotype 
# FYPO:0002151 inviable spore
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "178."
perl -pi -e 's/ESSENTIAL spores- germinated spores- small colonies long cells at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 179 ****** asked jacky about penetracne
# ESSENTIAL spores- germinated spores- often long at 25-32
# ESSENTIAL spores- germinated spores slightly long at 25-32
# broad phenotype: long high penetrance 
# cell phenotype
# FYPO:0000314 inviable after spore germination with elongated germ tube 
# FYPO:0002151 inviable spore 
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "179."
perl -pi -e 's/ESSENTIAL spores- germinated spores- often long at 25-32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0000310,PECO:0000005| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly long at 25-32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 180.
# ESSENTIAL germinated spores- occasionally long- some microcolonies of long cells at 25-32
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# FYPO:0000314 inviable after spore germination with elongated germ tube (low penetrance)
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "180."
perl -pi -e 's/ESSENTIAL germinated spores- occasionally long- some microcolonies of long cells at 25-32/FYPO:0000310,PECO:0000005| FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 181.
# ESSENTIAL microcolonies long misshapen cells at 25-32- may be giving rise to suppressors
# ESSENTIAL microcolonies long misshapen cells at 25-32
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell, interphase block  (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "181."
perl -pi -e 's/ESSENTIAL microcolonies long misshapen cells at 25-32- may be giving rise to suppressors/FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies long misshapen cells at 25-32/FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 182.
# ESSENTIAL spores- germinated spores- some microcolonies long cells at 25-32
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0002151 inviable spore (low penetrance)
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology 
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell, interphase block (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "182."
perl -pi -e 's/ESSENTIAL spores- germinated spores- some microcolonies long cells at 25-32/FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000310,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 183.
# ESSENTIAL germinated spores- often long at 25-32
# ESSENTIAL germinated spores- often long often divide at 25- 32 
# ESSENTIAL germinated spores- often long- some division at 25-32
# jacky says slightly less penetrant but still high pentrant
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology (low penetrance)
# FYPO:0002379 inviable after spore germination, without cell division, with elongated germ tube  (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression
# FYPO:0002724 inviable after spore germination, single or double cell division, elongated cell
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "183."
perl -pi -e 's/ESSENTIAL germinated spores- often long at 25-32/FYPO:0000310,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002379,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores- often long often divide at 25- 32/FYPO:0000310,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002379,has_penetrance(FYPO_EXT:0000003)| FYPO:0002724,PECO:0000005| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores- often long- some division at 25-32/FYPO:0000310,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002379,has_penetrance(FYPO_EXT:0000003)| FYPO:0002724,PECO:0000005| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 184
# ESSENTIAL spores, germinated spores long at 25,32
# ESSENTIAL spores- germinated spores- occasionally long- occasionally microcolonies long cells at 25-32
# broad phenotype: long low penetrance 
# cell phenotype
# FYPO:0000314 inviable after spore germination with elongated germ tube (low penetrance)
# FYPO:0002151 inviable spore (high penetrnace)
# FYPO:0000059 abnormal mitotic cell cycle progression
# population phenotype
# FYPO:0002061 inviable vegetative cell population
# echo "184."
perl -pi -e 's/ESSENTIAL spores- germinated spores long at 25-32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores- occasionally long- occasionally microcolonies long cells at 25-32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 185.
# a) ESSENTIAL spores- germinated spores slightly misshapen divide once at 25-32
# b) ESSENTIAL spores- germinated spores slightly misshapen divide once  at 25-32
# c) ESSENTIAL spores- germinated spores slightly misshapen may divide once at 25-32
# d) ESSENTIAL spores- germinated spores slightly misshapen- divides once at 25-32
# e) ESSENTIAL spores- germinated spores slightly misshapen often divides once at 25-32
# f) ESSENTIAL spores- germinated spores slightly misshapen- occasionally divide at 25-32
# g) ESSENTIAL spores- some germinated spores slightly misshapen divide once at 25-32
# h) ESSENTIAL spores- germinated spores slightly misshapen- some division at 25-32 
# i) ESSENTIAL spores- germinated spores divide once at 32- microcolonies misshapen cells at 25
# broad classifier: misshapen essential
# cell phenotype
# FYPO:0002151 inviable spore
# FYPO:0002420 inviable after spore germination, single cell division, abnormal cell shape 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "185a."
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen divide once at 25-32/FYPO:0002151,PECO:0000005 | FYPO:0002420,PECO:0000005|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "185b."
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen divide once  at 25-32/FYPO:0002151,PECO:0000005 | FYPO:0002420,PECO:0000005|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "185c."
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen may divide once at 25-32/FYPO:0002151,PECO:0000005 | FYPO:0002420,PECO:0000005|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "185d."
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen- divides once at 25-32/FYPO:0002151,PECO:0000005 | FYPO:0002420,PECO:0000005|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "185e."
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen often divides once at 25-32/FYPO:0002151,PECO:0000005 | FYPO:0002420,PECO:0000005|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "185f."
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen- occasionally divide at 25-32/FYPO:0002151,PECO:0000005 | FYPO:0002420,PECO:0000005|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "185g."
perl -pi -e 's/ESSENTIAL spores- some germinated spores slightly misshapen divide once at 25-32/FYPO:0002151,PECO:0000005 | FYPO:0002420,PECO:0000005|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "185h."
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen- some division at 25-32/FYPO:0002151,PECO:0000005 | FYPO:0002420,PECO:0000005|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "185i."

# *********check this one
# add FYPO:0002148 inviable after spore germination, multiple cell divisions, abnormal morphology
perl -pi -e 's/ESSENTIAL spores- germinated spores divide once at 32- microcolonies misshapen cells at 25/FYPO:0002151,PECO:0000005 | FYPO:0002420,PECO:0000005|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv


# 186.
# ESSENTIAL germinated spores long- microcolonies WT cells at 25-32
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0002379 inviable after spore germination, without cell division, with elongated germ tube (high pen)
# FYPO:0001110 inviable after spore germination, multiple cell divisions, normal morphology (low pen)
# FYPO:0000059 abnormal mitotic cell cycle progression
# population phenotype
#  FYPO:0002061 inviable vegetative cell population
echo "186."
perl -pi -e 's/ESSENTIAL germinated spores long- microcolonies WT cells at 25-32/FYPO:0002379,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|  FYPO:0001110,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 187.
# # DIVIDE ONCE OR TWICE
# 8 ESSENTIAL germinated spores slightly misshapen and divide once or twice at 25-32
# 1 ESSENTIAL germinated spores slightly misshapen- divide once or twice at 25-32
# 2 ESSENTIAL germinated spores slightly misshapen- occasionally divide once or twice- at 25-32
# add FYPO:0000313 inviable after spore germination, without cell division, with abnormal germ tube morphology
# broad classifier: Misshapen essential
# cell phenotype
# FYPO:0002421 inviable after spore germination, single or double cell division, abnormal shape cells (low expressivity)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "187."
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen and divide once or twice at 25-32/FYPO:0002421,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen- divide once or twice at 25-32/FYPO:0002421,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen- occasionally divide once or twice- at 25-32/FYPO:0000313,PECO:0000005| FYPO:0002421,PECO:0000005,has_penetrance(FYPO_EXT:0000003)|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# echo "188."
# ESSENTIAL germinated spores slightly misshapen septated- often divide once at 25-32
# broad classifier: misshapen essential
# cell phenotype
# FYPO:0002420 inviable after spore germination, single cell division, abnormal morphology 
# FYPO:0002423 inviable after spore germination, without cell division, septated cells with abnormal cell shape 
# population phenotpe
# FYPO:0002061 inviable vegetative cell population
echo "188."
perl -pi -e 's/ESSENTIAL germinated spores slightly misshapen septated- often divide once at 25-32/FYPO:0002420,PECO:0000005| FYPO:0002423,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 189.
# broad classifier: Misshapen essential
# ESSENTIAL spores- germinated spores slightly misshapen- some division at 25-32
# ESSENTIAL spores- germinated spores slightly misshapen- occasionally divide once at 25-32
# cell phenotype
# FYPO:0002151 inviable spore
# FYPO:0002420 inviable after spore germination, single cell division, abnormal morphology 
# FYPO:0000313 inviable after spore germination, without cell division, with abnormal germ tube morphology 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "189."
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen- some division at 25-32/FYPO:0002151,PECO:0000005| FYPO:0002420,PECO:0000005| FYPO:0000313,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen- occasionally divide once at 25-32/FYPO:0002151,PECO:0000005| FYPO:0002420,PECO:0000005| FYPO:0000313,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 190.
# ESSENTIAL spores- germinated spores- occasionally microcolonies misshapen cells at 25-32
# ESSENTIAL spores- germinated spores- some microcolonies slightly misshapen cells at 25-32
# ESSENTIAL germinated spores- occasionally microcolonies misshapen cells at 25-32  (no spore term for this one)
# broad classifier: germination
# cell phenotype
# FYPO:0002151 inviable spore (low penetrance)
# FYPO:0001991 inviable after spore germination, without cell division (high penetrance)
# FYPO:0001511 inviable vegetative cell, abnormal cell shape, normal cell size (low penetrance)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "190."
perl -pi -e 's/ESSENTIAL spores- germinated spores- occasionally microcolonies misshapen cells at 25-32/FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0001991,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001511,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores- some microcolonies slightly misshapen cells at 25-32/FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0001991,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001511,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores- occasionally microcolonies misshapen cells at 25-32/FYPO:0001991,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001511,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 191.
# ESSENTIAL spores- germinated spores- microcolonies slightly misshapen cells at 25-32
# broad classifier: misshapen
# cell phenotype
# FYPO:0002151 inviable spore (low penetrance)
# FYPO:0001991 inviable after spore germination, without cell division (low penetrance)
# FYPO:0001511 inviable vegetative cell, abnormal cell shape, normal cell size (high penetrance)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "190."
perl -pi -e 's/ESSENTIAL spores- germinated spores- microcolonies misshapen cells at 25-32/FYPO:0002151,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0001991,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0001511,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 192.
# 
# broad classifier: misshapen essential
# ESSENTIAL germinated spores- some microcolonies misshapen cells at 25-32
# ESSENTIAL germinated spores- microcolonies misshapen cells at 25-32
# cell phenotype
# FYPO:0001991 inviable after spore germination, without cell division
# FYPO:0002429 inviable germinated spore, multiple cell divisions, abnormal shape (normal size)  
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "192."
perl -pi -e 's/ESSENTIAL germinated spores- some microcolonies misshapen cells at 25-32/FYPO:0001991,PECO:0000005| FYPO:0002429,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores- microcolonies misshapen cells at 25-32/FYPO:0001991,PECO:0000005| FYPO:0002429,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 193.
# ESSENTIAL spores- microcolonies misshapen cells at 25-32
# broad classifier:  misshapen essential
# cell phenotype
# FYPO:0002151 inviable spore
# FYPO:0002429 inviable germinated spore, multiple cell divisions, abnormal shape (normal size)  
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "193."
perl -pi -e 's/ESSENTIAL spores- microcolonies misshapen cells at 25-32/FYPO:0002151,PECO:0000005| FYPO:0002429,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 194.
# broad classifier: misshapen essential
# ESSENTIAL spores- germinated spores- often misshapen at 25-32
# ESSENTIAL spores- germinated spores misshapen at 25-32
# ESSENTIAL spores- germinated spores slightly misshapen at 25-32
# cell phenotype
# FYPO:0002151 inviable spore
# FYPO:0002429 inviable germinated spore, multiple cell divisions, abnormal shape (normal size)  
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "194."
perl -pi -e 's/ESSENTIAL spores- germinated spores- often misshapen at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000313,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores misshapen at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000313,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000313,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 195.
# ESSENTIAL small colonies misshapen cells at 25,32, small colonies rounded cells at 36 possibly gives rise to suppressors
# ESSENTIAL small colonies misshapen cells at 25-32
# ESSENTIAL small colonies slightly misshapen cells at 25-32
# ESSENTIAL small colonies slightly misshapen cells- sporulating- lysis at 25-32
# broad classifier: misshapen essential
# cell phenotype
# FYPO:0002148 inviable after spore germination, multiple cell divisions, abnormal morphology
# FYPO:0001887 sporulation in haploid
# FYPO:0000647 cell lysis
# FYPO:0002187 inviable normal volume spheroid vegetative cell   (high temp)  
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "195."
perl -pi -e 's/ESSENTIAL small colonies misshapen cells at 25-32- small colonies rounded cells at 36 possibly gives rise to suppressors/FYPO:0002148,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002187,PECO:0000004| FYPO:0002061,PECO:0000005| FYPO:0002061,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL small colonies misshapen cells at 25-32/FYPO:0002148,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL small colonies slightly misshapen cells at 25-32/FYPO:0002148,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002021,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL small colonies slightly misshapen cells- sporulating- lysis at 25-32/FYPO:0002148,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005| FYPO:0001887,PECO:0000005| FYPO:0000647,PECO:0000005/g' tab_phenotype.csv

# 196
# misshapen essential
# ESSENTIAL microcolonies misshapen septated cells at 25-32 (3)
# ESSENTIAL microcolonies misshapen- septated cells at 25-32 (2)
# ESSENTIAL microcolonies septated misshapen cells at 32- cells  slightly misshapen at 25 (1)
# ESSENTIAL microcolonies septated misshapen cells at 32- cells  slightly misshapen at 25. (1)

# cell phenotype
# FYPO:0002451 inviable vegetative cell with abnormal cell shape
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "196."
perl -pi -e 's/ESSENTIAL microcolonies misshapen septated cells at 25-32/FYPO:0002451,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies misshapen- septated cells at 25-32/FYPO:0002451,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies septated misshapen cells at 32- cells  slightly misshapen at 25./FYPO:0002451,PECO:0000005|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies septated misshapen cells at 32- cells  slightly misshapen at 25/FYPO:0002451,PECO:0000005|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 197
# VIABLE skittle cells at 25-32
# VIABLE slightly skittle cells 25-32 (low expressivity)
# VIABLE small colonies slightly skittle slightly curved cells at 25-32
# cell phenotype
# FYPO:0002110 viable bottle-shaped vegetative cell
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "197."
perl -pi -e 's/VIABLE skittle cells at 25-32/FYPO:0002110,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly skittle cells 25-32/FYPO:0002110,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies slightly skittle slightly curved cells at 25-32/FYPO:0002110,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 198
# VIABLE long branched septated cells at 25-32
# VIABLE slightly long highly branched septated cells at 25-32
# VIABLE very small colonies branched septated slightly long cells  at 32 (at high temp only? asked JAcky****)
# VIABLE very small colonies branched- septated slightly long cells at 32 (at high temp only? asked JAcky ****)
# cell phenotype
# FYPO:0001512 branched, elongated cell
# population phenotype
# FYPO:0002060 viable vegetative cell population 
echo "198."
perl -pi -e 's/VIABLE long branched septated cells at 25-32/FYPO:0001512,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly long highly branched septated cells at 25-32/FYPO:0001512,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies branched septated slightly long cells  at 32/FYPO:0001512,PECO:0000004| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies branched- septated slightly long cells at 32/FYPO:0001512,PECO:0000004| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 199
# VIABLE curved cells at 25-32
# cell phenotype
# FYPO:0002112 viable curved cell
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "199."
perl -pi -e 's/VIABLE curved cells at 25-32/FYPO:0002112,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 200
# VIABLE WT cells occasionally curved at 25-32
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology
# FYPO:0002112 viable curved cell (low penetrance)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "200."
perl -pi -e 's/VIABLE WT cells occasionally curved at 25-32/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|FYPO:0002112,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 201a
# VIABLE stubby septated cells at 25-32
# VIABLE stubby cells at 32 cells barely growing at 25
# VIABLE stubby cells at 32 slightly misshapen cells at 25- misshapen cells at 36
# VIABLE slightly misshapen slightly stubby cells at 25-32 (low expressivity)
# VIABLE very small colonies stubby cells at 25-32
# VIABLE small colonies stubby cells at 25- microcolonies stubby septated cells at 32 (inviable at high T)
# cell phenotype
# FYPO:0002106 viable stubby vegetative cell
# FYPO:0002107 stubby inviable cell (high temp)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "201.a"
perl -pi -e 's/VIABLE stubby septated cells at 25-32/FYPO:0002106,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE stubby cells at 32 cells barely growing at 25/FYPO:0002106,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE stubby cells at 32 slightly misshapen cells at 25- misshapen cells at 36/FYPO:0002106,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen slightly stubby cells at 25-32/FYPO:0002106,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies stubby cells at 25-32/FYPO:0002106,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies stubby cells at 25- microcolonies stubby septated cells at 32/FYPO:0002106,PECO:0000005,has_expressivity(FYPO_EXT:0000003),has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0002107,PECO:0000006/g' tab_phenotype.csv

# 201b
# VIABLE stubby cells- occasionally long at 25-32- more septated branched cells at 36
# cell phenotype
# FYPO:0002106 viable stubby vegetative cell
# FYPO:0001122 elongated vegetative cell
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "201b."
perl -pi -e 's/VIABLE stubby cells- occasionally long at 25-32- more septated branched cells at 36/FYPO:0002106,PECO:0000005| FYPO:0002060,PECO:0000005| FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv


# 202
# VIABLE long slightly misshapen cells at 25,32, cells longer often curved at 36
# VIABLE long slightly misshapen cells at 25-32
# VIABLE small colonies long misshapen cells at 25-32, cells grow better at 25
# VIABLE small colonies long misshapen cells at 25-32
# VIABLE small colonies long slightly misshapen cells at 32
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001492 viable elongated vegetative cell
# FYPO:0000059 viable curved elongated vegetative cell
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "202."
perl -pi -e 's/VIABLE long slightly misshapen cells at 25-32- cells longer often curved at 36/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0002215,PECO:0000004 | FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE long slightly misshapen cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies long misshapen cells at 25-32- cells grow better at 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies long misshapen cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies long slightly misshapen cells at 32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv


# 203
# ESSENTIAL microcolonies long branched septated cells at 25-32
# ESSENTIAL microcolonies branched septated cells- slightly long at 25-32
# ESSENTIAL microcolonies long branched- septated cells at 25-32
# ESSENTIAL microcolonies misshapen branched septated slightly long cells at 25-32
# ESSENTIAL microcolonies misshapen slightly long cells- often branched septated at 25-32
# cell phenotype
# FYPO:0002170 inviable after spore germination, multiple cell divisions, branched, elongated cell
# population phenotype
# FYPO:0002061 inviable vegetative cell population   (MICROCOLONIES)
echo "203."
perl -pi -e 's/ESSENTIAL microcolonies long branched septated cells at 25-32/FYPO:0002170,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies branched septated cells- slightly long at 25-32/FYPO:0002170,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies long branched- septated cells at 25-32/FYPO:0002170,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies misshapen branched septated slightly long cells at 25-32/FYPO:0002170,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies misshapen slightly long cells- often branched septated at 25-32/FYPO:0002170,PECO:0000005|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 204
# ESSENTIAL microcolonies curved branched septated slightly long cells at 25-32
# ESSENTIAL microcolonies curved branched septated long cells at 25-32
# ESSENTIAL microcolonies curved septated branched slightly long cells at 25-32
# ESSENTIAL microcolonies curved branched septated slightly long cells at 25-32
# ESSENTIAL microcolonies long curved septated branched cells at 25-32
# cell phenotype
# FYPO:0002463 inviable branched, curved, elongated vegetative cell 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "204 a."
perl -pi -e 's/ESSENTIAL microcolonies curved branched septated slightly long cells at 25-32/FYPO:0002463,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
echo "204 b."
perl -pi -e 's/ESSENTIAL microcolonies curved branched septated long cells at 25-32/FYPO:0002463,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies curved septated branched slightly long cells at 25-32/FYPO:0002463,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies long curved septated branched cells at 25-32/FYPO:0002463,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 205 (Asked JAcky)
# ESSENTIAL spores- germinated spores long- some division at 25-32
# ESSENTIAL spores- germinated spores- occasionally long some division at 25-32
# ESSENTIAL spores- germinated spores long- microcolonies long cells at 25-32
# ESSENTIAL spores- germinated spores- often long at 25 some division at 32
# ESSENTIAL spores- germinated spores slightly misshapen occasionally long- some division at 25-32 (was classed as misshapen essential)
# ESSENTIAL spores- germinated spores long at 25- some division at 32
# broad phenotype: long low penetrance
# cell phenotype
# FYPO:0002379 inviable after spore germination, without cell division, with elongated germ tube
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# FYPO:0001110 inviable after spore germination, multiple cell divisions, normal morphology
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell, interphase block
# FYPO:0002151 inviable spore
# ADD THIRD CELL PHENOTYPE, ASKED JACKY
# inviable after spore germination, multiple cell divisions, normal morphology (low penetrance?) CHECK
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "205."
perl -pi -e 's/ESSENTIAL spores- germinated spores long- some division at 25-32/FYPO:0002379,PECO:0000005| FYPO:0002151,PECO:0000005| FYPO:0001110,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores- occasionally long some division at 25-32/FYPO:0002379,PECO:0000005| FYPO:0002151,PECO:0000005| FYPO:0001110,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores long- microcolonies long cells at 25-32/FYPO:0002379,PECO:0000005| FYPO:0002151,PECO:0000005| FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores- often long at 25 some division at 32/FYPO:0002379,PECO:0000005| FYPO:0002151,PECO:0000005| FYPO:0001110,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen occasionally long- some division at 25-32/FYPO:0002151,PECO:0000005| FYPO:0002379, PECO:0000005| FYPO:0001110,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores long at 25- some division at 32/FYPO:0002151,PECO:0000005| FYPO:0002379,PECO:0000005| FYPO:0001110,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 205 b
# ESSENTIAL germinated spores misshapen- microcolonies with some long cells at 25-32
# broad classifier: misshapen essential (could be long low pen)
# cell phenotype
# FYPO:0000313 inviable after spore germination, without cell division, with abnormal germ tube morphology
# FYPO:0001490 inviable elongated vegetative cell has_penetrance(FYPO_EXT:0000001)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "205b."
perl -pi -e 's/ESSENTIAL germinated spores misshapen- microcolonies with some long cells at 25-32/FYPO:0000313,PECO:0000005| FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 206
# ESSENTIAL spores misshapen at 25-32
# broad classifier : essential misshapen
# cell phenotype
# FYPO:0002427 inviable spore with abnormal shape 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "206."
perl -pi -e 's/ESSENTIAL spores misshapen at 25-32/FYPO:0002427,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 207   asked Jacky about penetrance **********
# ESSENTIAL spores- germinated spores- microcolonies slightly misshapen cells at 25-32
# ESSENTIAL spores- germinated spores- occasionally microcolonies slightly misshapen at 25-32
# ESSENTIAL spores- germinated spores- microcolonies slightly misshapen- vacuolated cells at 25-32 (Add vacuolated)
# ESSENTIAL spores- germinated spores slightly misshapen- often septated at 25-32
# ESSENTIAL spores- germinated spores- microcolonies slightly misshapen septated cells at 25-32
# broad phenotype: misshapen essential
# cell phenotype
# FYPO:0002151 inviable spore (COULD BE NORMAL SHAPE AND SIZE)
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# FYPO:0002429 inviable after spore germination, multiple cell divisions, abnormal cell shape, normal cell size
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "207."
perl -pi -e 's/ESSENTIAL spores- germinated spores- microcolonies slightly misshapen cells at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0002429,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores- occasionally microcolonies slightly misshapen at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0002429,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores- microcolonies slightly misshapen- vacuolated cells at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0002429,PECO:0000005| FYPO:0002410,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen- often septated at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0002429,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores- microcolonies slightly misshapen septated cells at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0002429,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv


# 208 
# ESSENTIAL spores  at 32- microcolonies skittle cells at 25
# broad phenotype: skittle
# cell phenotype
# FYPO:0002151 inviable spore (at high temperature)
# FYPO:0002109 inviable bottle-shaped cell (at low temperature)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "208."
perl -pi -e 's/ESSENTIAL spores  at 32- microcolonies skittle cells at 25/FYPO:0002151,PECO:0000004| FYPO:0002109,PECO:0000006| FYPO:0002061,PECO:0000006| FYPO:0002061,PECO:0000004/g' tab_phenotype.csv


# 209 
# ESSENTIAL microcolonies long cells- often misshapen at 25-32
# ESSENTIAL microcolonies long cells at 25- small colonies long cells at 32
# ESSENTIAL microcolonies slightly long cells-many dead cells at 25-32
# ESSENTIAL microcolonies long cells at 25- cells more misshapen at 32
# ESSENTIAL microcolonies long cells- possibly diploids at 25-32 (******asked JAcky about diploids)
# broad phenotype: long high penetrance
# cell phenotype
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell, interphase block
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "209."
perl -pi -e 's/ESSENTIAL microcolonies long cells- often misshapen at 25-32/FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies long cells at 25- small colonies long cells at 32/FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies slightly long cells-many dead cells at 25-32/FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies long cells at 25- cells more misshapen at 32/FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies long cells- possibly diploids at 25-32/FYPO:0003529,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 210 
# ESSENTIAL microcolonies long- wide cells at 25-32
# ESSENTIAL microcolonies slightly long and wide cells at 25-32
# ESSENTIAL microcolonies long wide cells at 25-32
# ESSENTIAL microcolonies wide- long cells at 25-32
# ESSENTIAL microcolonies long wide cells at 25-32
# ESSENTIAL microcolonies long wide cells at 25-32
# broad phenotype:  long high penetrance
# cell phenotype
# FYPO:0002251 inviable swollen elongated vegetative cell
# FYPO:0001490 inviable elongated vegetative cell
# FYPO:0000059 abnormal mitotic cell cycle progression
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "209."
perl -pi -e 's/ESSENTIAL microcolonies long- wide cells at 25-32/FYPO:0002251,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies slightly long and wide cells at 25-32/FYPO:0002251,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies long wide cells at 25-32/FYPO:0002251,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies wide- long cells at 25-32/FYPO:0002251,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies long wide cells at 25-32/FYPO:0002251,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies long wide cells at 25-32/FYPO:0002251,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 210 
# ESSENTIAL microcolonies long septated misshapen cells at 25- cells wider at 32 (at high temperature)
# broad phenotype: 
# cell phenotype
# FYPO:0002251 inviable swollen elongated vegetative cell (at high term)
# FYPO:0001490 inviable elongated vegetative cell
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "210."
perl -pi -e 's/ESSENTIAL microcolonies long septated misshapen cells at 25- cells wider at 32/FYPO:0002251,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005|  FYPO:0002061,PECO:0000004/g' tab_phenotype.csv

# 211 
# VIABLE rounded cells at 25,32, possibly ESSENTIAL and gives rise to suppressors
# VIABLE rounded cells at 25,32, better growth at 25
# VIABLE rounded cells at 25,32
# VIABLE very small colonies rounded cells at 32
# broad phenotype: rounded
# cell phenotype
# FYPO:0002380 viable spheroid vegetative cell
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "211."
perl -pi -e 's/VIABLE rounded cells at 25-32- possibly ESSENTIAL and gives rise to suppressors/FYPO:0002380,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE rounded cells at 25-32- better growth at 25/FYPO:0002380,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE rounded cells at 25-32/FYPO:0002380,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies rounded cells at 32/FYPO:0002380,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 212
#  ESSENTIAL microcolonies misshapen cells- often long at 25-32
# broad phenotype: 
# cell phenotype
# FYPO:0001490 inviable elongated vegetative cell (low penetrance)
# FYPO:0001489 inviable vegetative cell
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "212."
perl -pi -e 's/ESSENTIAL microcolonies misshapen cells- often long at 25-32/FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0001489,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv


# 213 (checking with Jacky********)
# ESSENTIAL germinated spores misshapen- some division at 25-32
# broad phenotype: essential misshapen
# cell phenotype
# FYPO:0000313 inviable after spore germination, without cell division, with abnormal germ tube morphology
# FYPO:0001042 inviable after spore germination, single or double cell division (low penetrance) ((ask Jacky what is shape like?)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "213."
perl -pi -e 's/ESSENTIAL germinated spores misshapen- some division at 25-32/FYPO:0000313,PECO:0000005| FYPO:0001042,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 214
# ESSENTIAL spores- germinated spores- small colonies long cells at 32
# broad phenotype: long low penetrance
# cell phenotype
# FYPO:0001490 inviable elongated vegetative cell
# FYPO:0002151 inviable spore
# FYPO:0001991 inviable after spore germination, without cell division
# FYPO:0000059 abnormal mitotic cell cycle progression
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "214."
perl -pi -e 's/ESSENTIAL spores- germinated spores- small colonies long cells at 32/FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001991,PECO:0000005| FYPO:0002151,PECO:0000005| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 215
# ESSENTIAL microcolonies slightly misshapen cells, some long cells at 32, long cells at 25
# ESSENTIAL microcolonies slightly misshapen cells- some long cells at 32
# broad phenotype: long, low penetrance
# cell phenotype
# FYPO:0001490 inviable elongated vegetative cell ( at high temp)
# FYPO:0002273 inviable vegetative cell with abnormal cell morphology (standard temp)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "215."
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells- some long cells at 32- long cells at 25/FYPO:0001490,PECO:0000004,has_penetrance(FYPO_EXT:0000003)| FYPO:0002273,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells- some long cells at 32/FYPO:0001490,PECO:0000004,has_penetrance(FYPO_EXT:0000003)| FYPO:0002273,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000004/g' tab_phenotype.csv

# 216 
# ESSENTIAL germinated spores long- often branched at 25-32
# ESSENTIAL germinated spores- often long and branched at 25-32
# ESSENTIAL germinated spores branched slightly long- septated at 25-32
# ESSENTIAL germinated spores swollen branched slightly long at 25-32 (same but add swollen)
# ESSENTIAL germinated spores very large swollen branched- initially germinated spores long at 25-32 (same but add swollen)
# ESSENTIAL very swollen branched germinated spores- initially germinated spores long at 25-32 
# broad phenotype: long branched
# cell phenotype
# FYPO:0002515 inviable after spore germination, without cell division, with elongated, branched germ tube 
# 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/1284/
echo "216."
perl -pi -e 's/ESSENTIAL germinated spores long- often branched at 25-32/FYPO:0002515,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores- often long and branched at 25-32/FYPO:0002515,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores branched slightly long- septated at 25-32/FYPO:0002515,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores swollen branched slightly long at 25-32/FYPO:0002515,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0003005,PECO:0000005| FYPO:0002061,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores very large swollen branched- initially germinated spores long at 25-32/FYPO:0002515,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0003005,PECO:0000005| FYPO:0002061,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL very swollen branched germinated spores- initially germinated spores long at 25-32/FYPO:0002515,PECO:0000004,has_penetrance(FYPO_EXT:0000001)| FYPO:0003005,PECO:0000005| FYPO:0002061,PECO:0000004/g' tab_phenotype.csv

# 217
# ESSENTIAL spores- germinated spores at 32- germinated spores often long at 25
# broad phenotype: long low penetrance
# cell phenotype
# FYPO:0002151 inviable spore (at high temp) 
# FYPO:0001991 inviable after spore germination, without cell division  (at high temp) (standard temp)
# FYPO:0002379 inviable after spore germination, without cell division, with elongated germ tube (standard temp) (low temp)
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "217."
perl -pi -e 's/ESSENTIAL spores- germinated spores at 32- germinated spores often long at 25/FYPO:0002151,PECO:0000004| FYPO:0001991,PECO:0000004| FYPO:0001991,PECO:0000005| FYPO:0002379,PECO:0000005| FYPO:0002379,PECO:0000003| FYPO:0002061,PECO:0000005,PECO:0000004| FYPO:0002061,PECO:0000006| FYPO:0000059/g' tab_phenotype.csv


# 218
# ESSENTIAL germinated spores long at 32- microcolonies long cells at 25
# 206 
# 
# broad phenotype: long high penetrance
# cell phenotype
# FYPO:0001490 inviable elongated vegetative cell (low temp) (high pen)
# FYPO:0000314 inviable after spore germination with elongated germ tube (standard temp) (high temp)
# FYPO:0000059 abnormal mitotic cell cycle progression
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "218."
perl -pi -e 's/ESSENTIAL germinated spores long at 32- microcolonies long cells at 25/FYPO:0001490,PECO:0000006,has_penetrance(FYPO_EXT:0000001)| FYPO:0000314,PECO:0000004| FYPO:0000314,PECO:0000005| FYPO:0002061,PECO:0000005| FYPO:0002061,PECO:0000006| FYPO:0000314,PECO:0000004| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 219
# ESSENTIAL germinated spores- microcolonies long cells at 25-32
# broad phenotype: long high penetrance
# cellphenotype
# FYPO:0001991 inviable after spore germination, without cell division
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell, interphase block
# FYPO:0000059 abnormal mitotic cell cycle progression  
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "219."
perl -pi -e 's/ESSENTIAL germinated spores- microcolonies long cells at 25-32/FYPO:0001991,PECO:0000005| FYPO:0001490,PECO:0000005| FYPO:0003529,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 220 
# ESSENTIAL microcolonies long cells- lysis at 25-32
# broad phenotype: long high penetrance
# cell phenotype
# FYPO:0001490 inviable elongated vegetative cell
# FYPO:0000647 cell lysis
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "220."
perl -pi -e 's/ESSENTIAL microcolonies long cells- lysis at 25-32/FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|  FYPO:0000647,PECO:0000005| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 220 
# ESSENTIAL microcolonies long cells- colonies appear dark at 25-32
# FYPO:0000059 abnormal mitotic cell cycle progression /Users/vw253/Desktop/IN PROGRESS PROJECTS
# broad phenotype: long high penetrance
# cell phenotype
# FYPO:0001490 inviable elongated vegetative cell
# FYPO:0000741 increased cellular pigment accumulation   (******** checkâother reasons?)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "220."
perl -pi -e 's/ESSENTIAL microcolonies long cells- colonies appear dark at 25-32/FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|  FYPO:0000741,PECO:0000005| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 221 
# ESSENTIAL germinated spores long- slight swollen at 25-32
# ESSENTIAL spores- germinated spores long wide at 25-32
# broad phenotype: 
# cell phenotype
# FYPO:0000059 abnormal mitotic cell cycle progression ???
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "221."
perl -pi -e 's/ESSENTIAL germinated spores long- slight swollen at 25-32/FYPO:0002911,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores long wide at 25-32/FYPO:0002151,PECO:0000005| FYPO:0002911,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv


# 222   ADD expressivity *******
# VIABLE small colonies slightly misshapen vacuolated cells at 25-32
# VIABLE slightly misshapen vacuolated cells at 25- 32
# VIABLE slightly misshapen vacuolated at 32
# VIABLE small colonies slightly misshapen, vacuolated cells at 25,32, some dead cells (***Ad something for dead cells)
# VIABLE small colonies slightly misshapen- vacuolated cells at 25-32
# VIABLE small colonies slightly misshapen- vacuolated cells a -32
# VIABLE slightly misshapen vacuolated cells at 25-32
# VIABLE slightly misshapen slightly vacuolated cells at 25-32
# VIABLE slightly misshapen vacuolated cells  at 32
# broad phenotype:  weak misshapen
# cell phenotype
# FYPO:0002476 viable vacuolated vegetative cell, abnormal cell shape, normal cell size
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "222."
perl -pi -e 's/VIABLE small colonies slightly misshapen vacuolated cells at 25-32/FYPO:0002476,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen vacuolated cells at 25- 32/FYPO:0002476,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen vacuolated at 32/FYPO:0002476,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies slightly misshapen- vacuolated cells at 25-32- some dead cells/FYPO:0002476,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies slightly misshapen- vacuolated cells at 25-32/FYPO:0002476,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies slightly misshapen- vacuolated cells a -32/FYPO:0002476,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen vacuolated cells at 25-32/FYPO:0002476,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen slightly vacuolated cells at 25-32/FYPO:0002476,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen vacuolated cells  at 32/FYPO:0002476,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 223 
# VIABLE WT cells- some dead cells at 25-32
# VIABLE WT cells- often dead cells at 25-32
# VIABLE WT cells- some dead cells at 32- WT cells at 25
# broad phenotype: WT
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology (high penetrance)
# FYPO:0001489 inviable vegetative cell (low penetrance)
# population phenotype
# FYPO:0002060 viable vegetative cell population 
echo "223."
perl -pi -e 's/VIABLE WT cells- some dead cells at 25-32/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001489,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE WT cells- often dead cells at 25-32/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001489,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE WT cells- some dead cells at 32- WT cells at 25/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0001489,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 224 
# VIABLE long septated cells- often multi septated at 25-32
# broad phenotype: long high penetrance
# cell phenotype
# FYPO:0001496 viable elongated multiseptate vegetative cell (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002060 viable vegetative cell population  
echo "224."
perl -pi -e 's/VIABLE long septated cells- often multi septated at 25-32/FYPO:0001496,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 225 
# VIABLE small colonies long septated cells at 25 32
# VIABLE long septated cells at 25,32, cells more branched at 36  (****ADD branched at high temp)
# VIABLE long septated cells at 25-32
# broad phenotype: long high penetrance
# cell phenotype
# FYPO:0001492 viable elongated vegetative cell
# FYPO:0000059 abnormal mitotic cell cycle
# FYPO:0002459 viable branched, elongated vegetative cell
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "225."
perl -pi -e 's/VIABLE small colonies long septated cells at 25 32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE long septated cells at 25-32- cells more branched at 36/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002459,PECO:0000004| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE long septated cells at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 226   *ask JAcky about this one*************** 
# VIABLE  WT cells- some germination long at 25-32
# 
# broad phenotype: 
# cell phenotype
# # FYPO:0000059 abnormal mitotic cell cycle progression 
# FYPO:0002177 viable cell with normal cell morphology (high penetrance)
# population phenotype
# FYPO:0002060	viable vegetative cell population
echo "21*."
perl -pi -e 's/VIABLE  WT cells- some germination long at 25-32/FYPO:0002177,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv


# 227 
# VIABLE small colonies WT cells- microcolonies skittle cells at 25-32
# VIABLE small colonies slightly misshapen cells- some microcolonies skittle cells at 25-32.
# VIABLE WT cells- microcolonies skittle cells at 25-32
# VIABLE skittle cells at 25- microcolonies skittle cells at 32
# VIABLE slightly skittle cells at 32- cells slightly misshapen at 25
# VIABLE slightly misshapen cells at 25- microcolonies skittle cells at 32
# broad phenotype:  skittle
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology
# FYPO:0002111 inviable bottle-shaped vegetative cell
# population phenotype
# FYPO:0002060,PECO:0000005

echo "227."
perl -pi -e 's/VIABLE small colonies WT cells- microcolonies skittle cells at 25-32/FYPO:0002177,PECO:0000005| FYPO:0002111,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies slightly misshapen cells- some microcolonies skittle cells at 25-32./FYPO:0002177,PECO:0000005|FYPO:0002111,PECO:0000005|  FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE WT cells- microcolonies skittle cells at 25-32/FYPO:0002177,PECO:0000005|FYPO:0002111,PECO:0000005|FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE skittle cells at 25- microcolonies skittle cells at 32/FYPO:0002177,PECO:0000005| FYPO:0002111,PECO:0000005|FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly skittle cells at 32- cells slightly misshapen at 25/FYPO:0002177,PECO:0000005| FYPO:0002111,PECO:0000005|FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen cells at 25- microcolonies skittle cells at 32/FYPO:0002177,PECO:0000005|FYPO:0002111,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 228.
# VIABLE slightly small cells at 25-32, cells slightly curved at 32, cells more curved at 36
# VIABLE slightly small cells at 25-32
# VIABLE slightly misshapen small cells at 25-32
# VIABLE slightly small cells at 32
# broad phenotype: 
# cell phenotype
# FYPO:0000648 viable small vegetative cell
# FYPO:0002405 viable curved stubby vegetative cell (high temp)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "228."
perl -pi -e 's/VIABLE slightly small cells at 25-32- cells slightly curved at 32- cells more curved at 36/FYPO:0000648,PECO:0000005| FYPO:0002060,PECO:0000005| FYPO:0002405,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly small cells at 25-32/FYPO:0000648,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen small cells at 25-32/FYPO:0000648,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly small cells at 32/FYPO:0000648,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv


# 229
# VIABLE small colonies long cells at 25- cells slightly misshapen at 32 (long low pen, was misshapen in spreadsheet)
# VIABLE very small colonies misshapen septated cells- occasionally long at 25-32 (long low pen (misshapen in spreadsheet)
# VIABLE small colonies long cells at 25-  cells barely grow at 32
# VIABLE small colonies slightly misshapen cells at 25 cells long misshapen 32 and lyses  (****addd lyses)
# VIABLE small colonies long misshapen cells at 32- cells slightly misshapen at 25
# VIABLE small colonies slightly long cells at 25- small colonies long cells at 32- microcolonies long cells at 36
# VIABLE slightly misshapen cells- often long at 25-32
# VIABLE small colonies WT cells- some long cells at 25-32- possibly diploidising
# VIABLE small colonies WT cells at 25- small colonies WT cells with some long cells at 32- very small colonies swollen long cells at 36 (add swollen at high temp)
# VIABLE small colonies long cells at 32, cells not so long long at 25
# VIABLE small colonies slightly misshapen- vacuolated cells- some long at 25-32 (add vacuolated)

# long high penetrance
# FYPO:0001492 viable elongated vegetative cell  (standard temp) (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression (standard temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population  (standard temp)
echo "229."
perl -pi -e 's/VIABLE small colonies long cells at 25- cells slightly misshapen at 32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies misshapen septated cells- occasionally long at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies long cells at 25-  cells barely grow at 32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies slightly misshapen cells at 25 cells long misshapen 32 and lyses/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies long misshapen cells at 32- cells slightly misshapen at 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies slightly long cells at 25- small colonies long cells at 32- microcolonies long cells at 36/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE slightly misshapen cells- often long at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies WT cells- some long cells at 25-32- possibly diploidising/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies WT cells at 25- small colonies WT cells with some long cells at 32- very small colonies swollen long cells at 36/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies long cells at 32- cells not so long long at 25/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies slightly misshapen- vacuolated cells- some long at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 230 
# VIABLE slightly misshapen cells- occasionally curved- occasionally long 25-32
# broad phenotype: long low pen
# cell phenotype
# FYPO:0001122 elongated vegetative cell  (standard temp) (low penetrance)
# FYPO:0002215 viable curved elongated vegetative cell
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "230."
perl -pi -e 's/VIABLE slightly misshapen cells- occasionally curved- occasionally long 25-32/FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002215,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

#230a
# VIABLE small colonies long cells- often curved at 25-32
# broad phenotype: long high pen
# cell phenotype
# FYPO:0001492 viable elongated vegetative cell  (standard temp) (high penetrance)
# FYPO:0002215 viable curved elongated vegetative cell (standard temp) (low penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002060 viable vegetative cell population

perl -pi -e 's/VIABLE small colonies long cells- often curved at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002215,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv


# 231. 
# VIABLE misshapen septated cells at 25-32
# VIABLE small colonies misshapen cells at 25- cells slightly misshapen at 32
# VIABLE small colonies misshapen septated at 32- cells less misshapen at 25
# VIABLE small colonies misshapen cells at 32- cells slightly misshapen at 25
# VIABLE misshapen septated cells at 32
# VIABLE very small colonies misshapen cells at 32
# VIABLE very small colonies misshapen cells at 25-32
# broad classifier: misshapen viable
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size  
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population 
echo "231."
perl -pi -e 's/VIABLE misshapen septated cells at 25-32/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies misshapen cells at 25- cells slightly misshapen at 32/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies misshapen septated at 32- cells less misshapen at 25/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE misshapen septated cells at 32/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies misshapen cells at 32- cells slightly misshapen at 25/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies misshapen cells at 32/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies misshapen cells at 25-32/FYPO:0001510,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 232  (ask JAcky if curved branched is also elongated ***********)
# VIABLE slightly misshapen cells at 25- small colonies misshapen cells at 32 some cells curved- branched at 36
# broad phenotype: misshapen viable
# cell phenotype
# FYPO:0001510 viable vegetative cell with abnormal cell shape, normal cell size (low expressivity)
# FYPO:0002477 viable branched, curved vegetative cell   https://sourceforge.net/p/pombase/fission-yeast-phenotype/984/ (low penetrance) (high temperature)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "232."
perl -pi -e 's/VIABLE slightly misshapen cells at 25- small colonies misshapen cells at 32 some cells curved- branched at 36/FYPO:0001510,PECO:0000005| FYPO:0002477,PECO:0000004| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 233  ****** ask JACky about penetracne
# VIABLE small colonies rounded misshapen cells- sporulating on YES  at 25,32 (added conjugation without glucose starvation)
# VIABLE rounded misshapen- septated cells at 25-32
# VIABLE rounded cells at 32- cells slightly misshapen at 25
# VIABLE small colonies rounded cells at 32, cells less rounded after 2 days growth (****include this?)
# VIABLE small colonies rounded cells at 32
# VIABLE small colonies rounded cells at 25- spores  at 32 (add spores at high temp? ask jacky, presumably inviable)
# broad phenotype: 
# cell phenotype
# FYPO:0002380  viable spheroid vegetative cell
# FYPO:0001864 conjugation without glucose starvation
# FYPO:0002060 viable vegetative cell population
echo "233."
perl -pi -e 's/VIABLE small colonies rounded misshapen cells- sporulating on YES at 25-32/FYPO:0002380,PECO:0000005| FYPO:0002060,PECO:0000005| FYPO:0001864,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE rounded misshapen- septated cells at 25-32/FYPO:0002380,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE rounded cells at 32- cells slightly misshapen at 25/FYPO:0002380,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies rounded cells at 32- cells less rounded after 2 days growth/FYPO:0002380,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies rounded cells at 32/FYPO:0002380,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies rounded cells at 25- spores  at 32/FYPO:0002380,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv


# 234
# VIABLE small colonies rounded and WT cells at 25-32 (check penetrance*********)
# VIABLE WT cells occasionally rounded at 25-32
# VIABLE WT cells at 25- rounded cells at 32- no colonies at 36 (inviable at high temperature)
# broad phenotype: 
# cell phenotype
# FYPO:0002380  viable spheroid vegetative cell
# FYPO:0002177 viable vegetative cell with normal cell morphology 
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "234."
perl -pi -e 's/VIABLE small colonies rounded and WT cells at 25-32/FYPO:0002380,PECO:0000005| FYPO:0002177,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE WT cells occasionally rounded at 25-32/FYPO:0002380,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002177,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE WT cells at 25- rounded cells at 32- no colonies at 36/FYPO:0002380,PECO:0000005| FYPO:0002177,PECO:0000005| FYPO:0002060,PECO:0000005| FYPO:0001489,PECO:0000004| FYPO:0002060,PECO:0000004/g' tab_phenotype.csv

# 235 
# VIABLE small colonies stubby curved cells at 32
# VIABLE stubby curved cells- aberrantly septated with misplaced septum at 25-32 (added misplaced septa) (we think this might be misleading for pom1, so omitted) SUPRESSED
# broad phenotype: 
# cell phenotype
# FYPO:0002405 viable curved stubby vegetative cell
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "235."
perl -pi -e 's/VIABLE small colonies stubby curved cells at 32/FYPO:0002405,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 236
# VIABLE WT cells at 25- stubby- septated cells at 32- cells dead at 36  PLUS inviable vegetative cell FYPO:0001489
# VIABLE small colonies WT cells at 25- stubby cells at 32
# broad phenotype: stubby
# cell phenotype
# FYPO:0002106 viable stubby vegetative cell
# FYPO:0002177 viable vegetative cell with normal cell morphology
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "236."
perl -pi -e 's/VIABLE WT cells at 25- stubby- septated cells at 32- cells dead at 36/FYPO:0002106,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002177,PECO:0000005| FYPO:0001489,PECO:0000004| FYPO:0002060,PECO:0000005| FYPO:0002061,PECO:0000004/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies WT cells at 25- stubby cells at 32/FYPO:0002106,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002177,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 237
# VIABLE small colonies slightly small cells at 25-32
# VIABLE small colonies small cells at 25-32- very small colonies at 36
# broad phenotype:  small
# cell phenotype 
# FYPO:0000648 viable small vegetative cell
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "21*."
perl -pi -e 's/VIABLE small colonies slightly small cells at 25-32/FYPO:0000648,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies small cells at 25-32- very small colonies at 36/FYPO:0000648,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 238 
# VIABLE slightly curved- slightly vacuolated cells at 32
# broad phenotype: curved
# cell phenotype
# FYPO:0002478 viable curved vacuolated vegetative cell  https://sourceforge.net/p/pombase/fission-yeast-phenotype/985/ 
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "238."
perl -pi -e 's/VIABLE slightly curved- slightly vacuolated cells at 32/FYPO:0002478,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 239
# VIABLE small colonies long cells- often branched at later times at 25-32 ******* later?
# broad phenotype: 
# cell phenotype
# FYPO:0001492 viable elongated vegetative cell
# FYPO:0002459 viable branched elongated vegetative cell 
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "239."
perl -pi -e 's/VIABLE small colonies long cells- often branched at later times at 25-32/FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002459,PECO:0000005| FYPO:0002060,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 240
# VIABLE  curved slightly long cells- occasionally T-shaped at 25-32
# VIABLE curved cells- some T-shaped-  aberrantly septated with septum often misplaced at 25- 32- cells longer at 36 (ask jacky about additions)
# VIABLE very small colonies slightly curved cells- occasionally T-shaped- often septated at 32 (low expressivity)
# broad phenotype: 
# cell phenotype
# FYPO:0002112 curved viable cell  (high penetrance)
# FYPO:0000013 T-shaped cell
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "240."
perl -pi -e 's/VIABLE  curved slightly long cells- occasionally T-shaped at 25-32/FYPO:0002112,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000013,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE curved cells- some T-shaped-  aberrantly septated with septum often misplaced at 25- 32- cells longer at 36/FYPO:0002112,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000013,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies slightly curved cells- occasionally T-shaped- often septated at 32/FYPO:0002112,PECO:0000005,has_penetrance(FYPO_EXT:0000001),has_expressivity(FYPO_EXT:0000003)| FYPO:0000013,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 241 # VIABLE small colonies WT cells- occasionally T-shaped cells- occasionally long at 25-32
# broad phenotype: long low penetrance
# cell phenotype
# FYPO:0000059 abnormal mitotic cell cycle progression (low penetrance, standard temp)
# FYPO:0001122 elongated viable vegetative cell (low penetrance, standard temp)
# FYPO:0002177 viable vegetative cell with normal cell morphology  
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "241."
perl -pi -e 's/VIABLE small colonies WT cells- occasionally T-shaped cells- occasionally long at 25-32/FYPO:0000059,PECO:0000005| FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0000013,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
 
# 241 
echo "241."

# 242 
# VIABLE small colonies long cells at 32- germinated spores long at 25
# VIABLE very small colonies long cells at 25- germinated spores long at 32
# broad phenotype: long high penetrance
# cell phenotype
# FYPO:0001492 elongated viable vegetative cell (high penetrance)
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/988/    
# FYPO:0002480 viable after spore germination, without cell division, with elongated germ tube 
# FYPO:0000059 abnormal mitotic cell cycle progression
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "242."
perl -pi -e 's/VIABLE small colonies long cells at 32- germinated spores long at 25/FYPO:0002480,PECO:0000006| FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE very small colonies long cells at 25- germinated spores long at 32/FYPO:0002480,PECO:0000004| FYPO:0001492,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 243 
# VIABLE slightly misshapen cells at 25- germinated spores  at 32  (inviable at high temp)
# VIABLE small colonies slightly misshapen cells at 25- small colonies long vacuolated cells at 32  (*****NOT CLASSED AS LONG&lt; WHY?)
# broad phenotype: 
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (low expressivity) (high penetrance)
# FYPO:0002379 inviable after spore germination, without cell division, with elongated germ tube
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "21*."
perl -pi -e 's/VIABLE slightly misshapen cells at 25- germinated spores  at 32/FYPO:0002379,PECO:0000004| FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE small colonies slightly misshapen cells at 25- small colonies long vacuolated cells at 32/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv


# 244 
# VIABLE slightly misshapen cells- initially branched septated slightly long- abnormal colony morphology at 25-32- cells dead at 36.
# broad phenotype: long branched
# cell phenotype 
# FYPO:0001512 branched, elongated cell
# FYPO:0000150 abnormal colony morphology
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "244."
perl -pi -e 's/VIABLE slightly misshapen cells- initially branched septated slightly long- abnormal colony morphology at 25-32- cells dead at 36./FYPO:0001512,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 245 
# VIABLE slightly misshapen multi septated cells at 25-32-cells grow better at 32 than 25  **** check combine cell phenotypes
# broad phenotype: 
# cell phenotype
# FYPO:0001510 viable vegetative cell, abnormal cell shape, normal cell size (low expressivity)
# FYPO:0000118 multiseptate
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "245."
perl -pi -e 's/VIABLE slightly misshapen multi septated cells at 25-32-cells grow better at 32 than 25/FYPO:0001510,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0000118,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 246
#  VIABLE WT cells- some germination long at 25-32- 
# broad phenotype: long low penetrance
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology  (high penetrance)
# FYPO:0002480 viable after spore germination with elongated germ tube (low pen)
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "246."
perl -pi -e 's/VIABLE WT cells- some germination long at 25-32-/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002480,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 247
# ESSENTIAL microcolonies curved cells- often long branched at 32- more division at 25 
# broad phenotype: 
# cell phenotype
# FYPO:0002113 inviable curved vegetative cell
# FYPO:0002481 inviable branched, curved vegetative cell 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "247."
perl -pi -e 's/ESSENTIAL microcolonies curved cells- often long branched at 32- more division at 25/FYPO:0002113,PECO:0000005| FYPO:0002481,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 248  ***** add penetrance
# ESSENTIAL microcolonies long septated cells- often curved and occasionally branched at 25-32
# broad phenotype: 
# cell phenotype
# FYPO:0001490 inviable elongated vegetative cell
# FYPO:0002411 inviable curved elongated vegetative cell
# FYPO:0002463 inviable branched, curved, elongated vegetative cell
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "248."
perl -pi -e 's/ESSENTIAL microcolonies long septated cells- often curved and occasionally branched at 25-32/FYPO:0001490,PECO:0000005| FYPO:0002411,PECO:0000005| FYPO:0002463,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 249
# ESSENTIAL  spores- germinated spores- occasionally divide at 25-32
# ESSENTIAL spores- germinated spores at 32- some colonies WT cells at 25
# broad phenotype germination
# cell phenotype
# FYPO:0002151  inviable spore
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# FYPO:0001042 inviable after spore germination, single or double cell division
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "249."
perl -pi -e 's/ESSENTIAL spores- germinated spores- occasionally divide at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores at 32- some colonies WT cells at 25/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 250
# ESSENTIAL spores- germinated spores at 32- microcolonies misshapen cells at 25
# broad phenotype germination
# cell phenotype
# FYPO:0002151  inviable spore
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# FYPO:0002061 inviable vegetative cell population
echo "250a."
perl -pi -e 's/ESSENTIAL spores- germinated spores at 32- microcolonies misshapen cells at 25/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0002061,PECO:0000006/g' tab_phenotype.csv

# 250
# ESSENTIAL spores- germinated spores- occasionally microcolonies small cells at 25-32
# broad phenotype germination
# cell phenotype
# FYPO:0002151  inviable spore
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# FYPO:0000951 inviable small vegetative cell
# population 
# FYPO:0002061 inviable vegetative cell population
echo "250b."
perl -pi -e 's/ESSENTIAL spores- germinated spores- occasionally microcolonies small cells at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0000951,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 251
# ESSENTIAL spores- germinated spores slightly misshapen divide once or twice at 25-32
# ESSENTIAL spores- germinated spores slightly misshapen divide once at 32
# ESSENTIAL spores- germinated spores misshapen lysis at 25-32 (miss division, add lysis)
#  ESSENTIAL spores- germinated spores slightly misshapen divide twice at 25-32 ( add divied twice)
# ESSENTIAL spores- germinated spores slightly misshapen may divide twice at 25-32
# broad phenotype 
# cell phenotype
# FYPO:0002151 inviable spore
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# FYPO:0001042 inviable after spore germination, single or double cell division
# FYPO:0002280 inviable after spore germination, single cell division
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "251."
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen divide once or twice at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen divide once at 32/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0002280,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores misshapen lysis at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0000647,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen divide twice at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores slightly misshapen may divide twice at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 252
# ESSENTIAL germinated spores- occasionally divide at 25-32
# ESSENTIAL germinated spores- some division at 25-32
# cell phenotype
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# FYPO:0001110 inviable after spore germination, multiple cell divisions, normal morphology
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "252."
perl -pi -e 's/ESSENTIAL germinated spores- occasionally divide at 25-32/FYPO:0000310,PECO:0000005| FYPO:0001110,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores- some division at 25-32/FYPO:0000310,PECO:0000005| FYPO:0001110,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv


# 253
# ESSENTIAL germinated spores at 32- microcolonies rounded cells at 25
# ESSENTIAL spores- germinated spores- occasional microcolonies of WT/ rounded cells at 25-32
# ESSENTIAL spores- germinated spores- often divide once to give rounded cells at 25-32
# cell phenotype
# FYPO:0002151 inviable spore
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# FYPO:0002482 inviable spheroid vegetative cell 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "253."
perl -pi -e 's/ESSENTIAL germinated spores at 32- microcolonies rounded cells at 25/FYPO:0000310,PECO:0000005| FYPO:0002151,PECO:0000005| FYPO:0002482,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores- occasional microcolonies of WT\/ rounded cells at 25-32/FYPO:0000310,PECO:0000005| FYPO:0002151,PECO:0000005| FYPO:0002482,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores- often divide once to give rounded cells at 25-32/FYPO:0000310,PECO:0000005| FYPO:0002151,PECO:0000005| FYPO:0002482,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 254
# ESSENTIAL spores- germinated spores- some long curved at 25-32
# broad classifier long low penetrance
# cell phenotype
# FYPO:0002151 inviable spore
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# FYPO:0002411 inviable curved elongated vegetative cell (low pen)
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "254."
perl -pi -e 's/ESSENTIAL spores- germinated spores- some long curved at 25-32/FYPO:0000310,PECO:0000005| FYPO:0002151,PECO:0000005| FYPO:0002411,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 255
# ESSENTIAL germinated spores- microcolonies slightly misshapen cells- some long cells at 25-32
# ESSENTIAL germinated spores- occasionally microcolonies slightly misshapen cells- some long cells at 25-32
# ESSENTIAL spores- germinated spores- occasionally microcolonies slightly misshapen cells- some long cells at 25-32 (same but add spores)
# ESSENTIAL spores- germinated spores- microcolonies slightly misshapen cells at 32- spores- germinated spores at 25 (as above but no long)
# broad classifier: long low pen
# cell phenotype
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# FYPO:0001490 inviable elongated vegetative cell (low pen)
# FYPO:0002273 inviable vegetative cell with abnormal cell morphology
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "255."
perl -pi -e 's/ESSENTIAL germinated spores- microcolonies slightly misshapen cells- some long cells at 25-32/FYPO:0000310,PECO:0000005| FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002273,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores- occasionally microcolonies slightly misshapen cells- some long cells at 25-32/FYPO:0000310,PECO:0000005| FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002273,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores- occasionally microcolonies slightly misshapen cells- some long cells at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002273,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores- microcolonies slightly misshapen cells at 32- spores- germinated spores at 25/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0002273,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 256
# ESSENTIAL microcolonies slightly misshapen cells-occasionally germinated spores long at 25-32
# ESSENTIAL microcolonies slightly misshapen cells- some long cells- some germinated spores long at 25-32
# ESSENTIAL microcolonies slightly misshapen cells- some germinated spores long at 25-32
# ESSENTIAL microcolonies slightly misshapen cells at 32- spores- germination at 25
# ESSENTIAL microcolonies slightly misshapen cells at 25- cells misshapen at 32
# broad classifier misshapen essential (why not long low pen?)
# FYPO:0000314 inviable after spore germination with elongated germ tube (low pen)
# FYPO:0002783 inviable vegetative cell with abnormal cell morphology (high pen)
# FYPO:0002451 inviable vegetative cell with abnormal cell shape
# population
# FYPO:0002061 inviable vegetative cell population
echo "256."
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells-occasionally germinated spores long at 25-32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002451,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells- some long cells- some germinated spores long at 25-32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002451,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells- some germinated spores long at 25-32/FYPO:0000314,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002451,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells at 32- spores- germination at 25/FYPO:0002451,PECO:0000005,has_penetrance(FYPO_EXT:0000001)|  FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells at 25- cells misshapen at 32/FYPO:0002451,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 257
# ESSENTIAL microcolonies slightly misshapen cells- some germinated spores long at 25-32 
# ESSENTIAL germinated spores long- microcolonies slightly misshapen cells- some long cells at 25-32
# ESSENTIAL germinated spores- microcolonies slightly misshapen cells  at 25-32 (but not elongated spores)
# broad phenotype: misshapen essential
# cell phenotype
# FYPO:0002379 inviable after spore germination, without cell division, with elongated germ tube
# FYPO:0002273 inviable vegetative cell with abnormal cell morphology 
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# FYPO:0001490 inviable elongated vegetative cell (low pen)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "257."
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells- some germinated spores long at 25-32/FYPO:0002379,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002273,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores long- microcolonies slightly misshapen cells- some long cells at 25-32/FYPO:0000310,PECO:0000005| FYPO:0002273,PECO:0000005| FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL germinated spores- microcolonies slightly misshapen cells  at 25-32/FYPO:0000310,PECO:0000005| FYPO:0002273,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 258
# ESSENTIAL germinated spores misshapen- microcolonies slightly misshapen cells- some long cells some misshapen septated cells at 25-32
# ESSENTIAL microcolonies slightly misshapen cells- some long cells at 25- germinated spores long at 32
# ESSENTIAL microcolonies misshapen cells- some germinated spores long at 25-32
# ESSENTIAL microcolonies slightly misshapen cells- some long cells- often misshapen at 25-32
# ESSENTIAL microcolonies slightly misshapen cells- some long cells- aberrantly septated with misplaced septum at 25-32
# broad phenotype: long low pen
# cell phenotype
# FYPO:0002281 inviable after spore germination with abnormal germ tube morphology
# FYPO:0002379 inviable after spore germination, without cell division, with elongated germ tube
# FYPO:0002273 inviable vegetative cell with abnormal cell morphology
# FYPO:0001490 inviable elongated vegetative cell (low pen)
# FYPO:0000059 abnormal mitotic cell cycle progression 
# FYPO:0000339 mislocalized septum
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "258."
perl -pi -e 's/ESSENTIAL germinated spores misshapen- microcolonies slightly misshapen cells- some long cells some misshapen septated cells at 25-32/FYPO:0002281,PECO:0000005| FYPO:0002273,PECO:0000005| FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells- some long cells at 25- germinated spores long at 32/FYPO:0002281,PECO:0000004| FYPO:0002273,PECO:0000005| FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies misshapen cells- some germinated spores long at 25-32/FYPO:0002379,PECO:0000004,has_penetrance(FYPO_EXT:0000003)| FYPO:0002273,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells- some long cells- often misshapen at 25-32/FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002273,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells- some long cells- aberrantly septated with misplaced septum at 25-32/FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002273,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000339,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 259 
# ESSENTIAL microcolonies small cells- often skittle at 25-32
# broad phenotype: skittle
# cell phenotype
# FYPO:0002483  inviable small bottle-shaped vegetative cell inviable https://sourceforge.net/p/pombase/fission-yeast-phenotype/993/
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "259."
perl -pi -e 's/ESSENTIAL microcolonies small cells- often skittle at 25-32/FYPO:0002483,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 260
# VIABLE WT cells at 25- ESSENTIAL microcolonies of skittle cells at 32-36
# broad phenotype: skittle
# cell phenotype
# FYPO:0002111 inviable bottle-shaped vegetative cell standard temp, high temp
# FYPO:0002177 viable vegetative cell with normal cell morphology, low temp
# population phenotype
# FYPO:0002060 viable vegetative cell population (standard temp)
# FYPO:0002061 inviable vegetative cell population (high temp)
echo "260."
perl -pi -e 's/VIABLE WT cells at 25- ESSENTIAL microcolonies of skittle cells at 32-36./FYPO:0002111,PECO:0000004| FYPO:0002111,PECO:0000004| FYPO:0002177,PECO:0000006| FYPO:0002060,PECO:0000005| FYPO:0002061,PECO:0000004| FYPO:0002111,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/VIABLE WT cells at 25- ESSENTIAL microcolonies of skittle cells at 32-36/FYPO:0002111,PECO:0000004| FYPO:0002111,PECO:0000004| FYPO:0002177,PECO:0000006| FYPO:0002060,PECO:0000005| FYPO:0002061,PECO:0000004| FYPO:0002111,PECO:0000005/g' tab_phenotype.csv

# 261
# ESSENTIAL microcolonies slightly misshapen septated cells at 32- cells slightly curved at 25
# 
# broad phenotype: curved
# cell phenotype
# FYPO:0002113 inviable curved vegetative cell (low temp)
# FYPO:0002273 inviable vegetative cell with abnormal cell morphology
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "261."
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen septated cells at 32- cells slightly curved at 25/FYPO:0002113,PECO:0000006| FYPO:0002273,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 262
# ESSENTIAL spores- germinated spores- occasionally microcolonies wee at 25-32
# broad phenotype: 
# cell phenotype
# FYPO:0002151 inviable spore
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology
# FYPO:0000951 inviable small vegetative cell (low pen)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "262."
perl -pi -e 's/ESSENTIAL spores- germinated spores- occasionally microcolonies wee at 25-32/FYPO:0002151,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0000951,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 263
# ESSENTIAL spores misshapen lysis at 25-32
# 
# broad phenotype: 
# cell phenotype
# FYPO:0002489 spore lysis  https://sourceforge.net/p/pombase/fission-yeast-phenotype/995/
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "263."
perl -pi -e 's/ESSENTIAL spores misshapen lysis at 25-32/FYPO:0002489,PECO:0000005| FYPO:0002489,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 264
# ESSENTIAL germinated spores swollen dumbbell shaped at 25-32 
# ESSENTIAL spores misshapen- swollen often dumbbell shaped at 25-32
# broad phenotype: misshapen essential
# cell phenotype
# FYPO:0002987 inviable after spore germination, without cell division, swollen dumbbell-shaped cell
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "264."
perl -pi -e 's/ESSENTIAL germinated spores swollen dumbbell shaped at 25-32/FYPO:0002987,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores misshapen- swollen often dumbbell shaped at 25-32/FYPO:0002987,PECO:0000005,has_expressivity(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv


# 265
# ESSENTIAL germinated spores long- swollen centre at 25-32 
# broad phenotype: misshapen essential
# cell phenotype
# FYPO:0002083 inviable swollen elongated cell with enlarged nucleus
# population phenotype 
# FYPO:0002061 inviable vegetative cell population
echo "265."
perl -pi -e 's/ESSENTIAL germinated spores long- swollen centre at 25-32/FYPO:0002083,PECO:0000005,has_expressivity(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 266
# ESSENTIAL germinated spores long- septated- some division and swollen cells at 25-32
# broad phenotype: misshapen essential
# cell phenotype
# FYPO:0000315 inviable after spore germination, without cell division, with elongated, septated germ tube
# FYPO:0002490 inviable after spore germination, multiple cell divisions, swollen cell https://sourceforge.net/p/pombase/fission-yeast-phenotype/996/
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "266."
perl -pi -e 's/ESSENTIAL germinated spores long- septated- some division and swollen cells at 25-32/FYPO:0000315,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 267
# ESSENTIAL spores- germinated spores- microcolonies long cells- occasionally misshapen branched at 25-32
# ESSENTIAL microcolonies long cells- some germinated spores 25-32
# broad phenotype: long high penetrance
# cell phenotype
# FYPO:0002170 inviable after spore germination, multiple cell divisions, branched, elongated cell (low pen)
# FYPO:0002463 viable branched, elongated vegetative cell  (high pen)
# FYPO:0000310 inviable after spore germination with normal germ tube morphology
# FYPO:0002151 inviable spore
# FYPO:0001490 inviable elongated vegetative cell 
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "267."
perl -pi -e 's/ESSENTIAL spores- germinated spores- microcolonies long cells- occasionally misshapen branched at 25-32/FYPO:0002170,PECO:0000005| FYPO:0002463,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0002151,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies long cells- some germinated spores 25-32/FYPO:0000310,PECO:0000005,has_penetrance(FYPO_EXT:0000003)|  FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 268
#  ESSENTIAL spores- some microcolonies slightly misshapen cells at 25-32
#  ESSENTIAL spores  at 32- microcolonies misshapen cells at 25
#  ESSENTIAL spores- germinated spores- some division slightly misshapen cells at 25-32
# broad phenotype: essential misshapen
# cell phenotype
# FYPO:0002151 inviable spore
# FYPO:0002451 inviable vegetative cell with abnormal cell shape (****check I use this for all ess  misshapen)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "268."
perl -pi -e 's/ESSENTIAL spores- some microcolonies slightly misshapen cells at 25-32/FYPO:0002151,PECO:0000005| FYPO:0002451,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores  at 32- microcolonies misshapen cells at 25/FYPO:0002151,PECO:0000005| FYPO:0002451,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL spores- germinated spores- some division slightly misshapen cells at 25-32/FYPO:0002151,PECO:0000005| FYPO:0002451,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 269
# ESSENTIAL small colonies misshapen cells- aberrantly septated with misplaced septum at 32- microcolonies long cells at 25
# ESSENTIAL microcolonies slightly misshapen cells- some long cells- some lysis at 25-32
# FYPO:0002451 inviable vegetative cell with abnormal cell shape
# *** add misplaced septa
# FYPO:0001122 elongated vegetative cell  (low temperature)
# FYPO:0000647 cell lysis (low penetrance) 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "269."
perl -pi -e 's/ESSENTIAL small colonies misshapen cells- aberrantly septated with misplaced septum at 32- microcolonies long cells at 25/FYPO:0001122,PECO:0000006| FYPO:0002451,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells- some long cells- some lysis at 25-32/FYPO:0001122,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002451,PECO:0000005| FYPO:0000647,PECO:0000005,has_penetrance(FYPO_EXT:0000003)| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 270
# ESSENTIAL microcolonies misshapen cells at 25- germinated spores  at 32
# cell phenotype
# FYPO:0002451 inviable vegetative cell with abnormal cell shape
# FYPO:0001991 inviable after spore germination, without cell division germinated spores 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "270."
perl -pi -e 's/ESSENTIAL microcolonies misshapen cells at 25- germinated spores  at 32/FYPO:0001991,PECO:0000006| FYPO:0002451,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 271
# ESSENTIAL germinated spores- often divide once to give one slightly misshapen cell and one dead cell at 25- 32
# cell phenotype
# FYPO:0002420 inviable after spore germination, single cell division, abnormal cell shape
# FYPO:0000310 inviable after spore germination, without cell division, with normal germ tube morphology  
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "271."
perl -pi -e 's/ESSENTIAL germinated spores- often divide once to give one slightly misshapen cell and one dead cell at 25- 32/FYPO:0002420,PECO:0000005| FYPO:0000310,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 272  ESSENTIAL small colonies slightly long misshapen cells- at 25- cells longer at 32
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0001490 inviable elongated vegetative cell (high penetrance)
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "272."
perl -pi -e 's/ESSENTIAL small colonies slightly long misshapen cells- at 25- cells longer at 32/FYPO:0001490,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002061,PECO:0000005| FYPO:0000059,PECO:0000005/g' tab_phenotype.csv

# 273 (asked jacky about chained)
# SPBC2G5.07c ESSENTIAL microcolonies slightly misshapen cells- aberrantly septated to give chains of 4 cells at 25-32
# cell phenotype
# FYPO:0001971 abnormal cytokinetic cell separation resulting in chained cells
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "273."
perl -pi -e 's/ESSENTIAL microcolonies slightly misshapen cells- aberrantly septated to give chains of 4 cells at 25-32/FYPO:0001971,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 274
# VIABLE stubby cells at 25- ESSENTIAL microcolonies with some long cells at 32
# broad classifier long low pen
# cell phenotype
# FYPO:0001490 inviable elongated vegetative cell 
# FYPO:0002106 viable stubby vegetative cell
# FYPO:0000059 abnormal mitotic cell cycle progression 
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "274."
perl -pi -e 's/VIABLE stubby cells at 25- ESSENTIAL microcolonies with some long cells at 32/FYPO:0001490,PECO:0000006,has_penetrance(FYPO_EXT:0000003)| FYPO:0002106,PECO:0000006| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 275
# ESSENTIAL germinated spores- some small colonies long cells at 25- microcolonies slightly misshapen cells- some long cells at 32
# broad classifier: long low pen
# cell phenotypes
# FYPO:0000059 abnormal mitotic cell cycle progression
# FYPO:0001492 inviable elongated vegetative cell
# FYPO:0001991 inviable after spore germination, without cell division germinated spores 
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "275."
perl -pi -e 's/ESSENTIAL germinated spores- some small colonies long cells at 25- microcolonies slightly misshapen cells- some long cells at 32/FYPO:0001492,PECO:0000006,has_penetrance(FYPO_EXT:0000003)| FYPO:0001991,PECO:0000005|  FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 276
# VIABLE small colonies WT cells at 25- ESSENTIAL spores- germinated spores at 32
# broad classifier: WT
# FYPO:0002177 viable vegetative cell with normal cell morphology  (high penetrance)
# FYPO:0000310 inviable after spore germination with normal germ tube morphology (high temp)
# FYPO:0002151 inviable spore (high temp)
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "276."
perl -pi -e 's/VIABLE small colonies WT cells at 25- ESSENTIAL spores- germinated spores at 32/FYPO:0002177,PECO:0000005| FYPO:0000310,PECO:0000004 |FYPO:0002151,PECO:0000004| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 277
# VIABLE slightly misshapen cells at 25- ESSENTIAL germinated spores long- often divide at 32
# broad classifier: long high penetrance
# FYPO:0002379 inviable after spore germination, without cell division, with elongated germ tube  (high penetrance)
# FYPO:0001042 inviable after spore germination, single or double cell division
# FYPO:0000059 abnormal mitotic cell cycle progression
# population phenotype
# FYPO:0002060 viable vegetative cell population
echo "277."
perl -pi -e 's/VIABLE slightly misshapen cells at 25- ESSENTIAL germinated spores long- often divide at 32/FYPO:0002379,PECO:0000005| FYPO:0001042,PECO:0000005| FYPO:0000059,PECO:0000005| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv

# 278
# 
# ESSENTIAL microcolonies long cells at 32- ESSENTIAL/VIABLE small colonies long misshapen cells at 25
# broad classifier: long high penetrance
# cell phenotype
# FYPO:0003529 inviable after spore germination, multiple cell divisions, elongated cell, interphase block
# FYPO:0000059 abnormal mitotic cell cycle progression
# population phenotype
# FYPO:0002061 inviable vegetative cell population
echo "278."
perl -pi -e 's/ESSENTIAL microcolonies long cells at 32- ESSENTIAL\/VIABLE small colonies long misshapen cells at 25/FYPO:0003529,PECO:0000006,has_penetrance(FYPO_EXT:0000001)| FYPO:0000059,PECO:0000005| FYPO:0002061,PECO:0000005/g' tab_phenotype.csv

# 279. DONE BUT SUBSTRING SO NEEDS TO BE NEAR BOTTOM (substring of lots)
# VIABLE WT cells at 25,32
# broad classifier WT
# https://sourceforge.net/p/pombase/fission-yeast-phenotype/824/
# cell phenotype
# FYPO:0002177 viable vegetative cell with normal cell morphology (high penetrance)
# poplulation phenotype
# FYPO:0002060 viable vegetative cell population
echo "279."
perl -pi -e 's/VIABLE WT cells at 25-32/FYPO:0002177,PECO:0000005,has_penetrance(FYPO_EXT:0000001)| FYPO:0002060,PECO:0000005/g' tab_phenotype.csv
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