After the next update, deprecrate this, BUT make a copy of the "supressed" annotations to seed the file of 'removals'

• Hayles et al Table S1 General Information and deletion phenotype description.xlsx

• In pombe-embl/phenotype_mapping

• cp phenotype.txt_with_tab tab_phenotype.csv (to refresh the file to parse)

• run /Users/val/Desktop/pombe-embl/phenotype_mapping/mapping.csh (converts the free text in JAckys spreadsheet to ontology terms) updates tab_phenotype.csv

• Split tab_phenotype.csv into one line per annotation

/Users/val/Desktop/pombe-embl/phenotype_mapping/one_liner.csh

• Convert this to phenotype input format

• ./scripts/mapping_to_phaf.pl ./one_line_per_annotation ./pombe_gene_name.txt > phaf_format_phenotypes.tsv

• The file "pombe_gene_name.txt" is created from Chado with these commands:

• \a
• \f '\t'
• \o pombe_gene_name.txt
• select uniquename, name from feature where organism_id = (select organism_id from organism where species = 'pombe') and type_id = (select cvterm_id from cvterm where name = 'gene');
• \o