wiki:PhenotypeMapping

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
Last modified 5 years ago Last modified on Apr 24, 2015, 11:47:49 AM