From c8fccf2c4527ca7308075f513631511fafaf652c Mon Sep 17 00:00:00 2001 From: athreyab Date: Sun, 29 Jan 2012 19:11:02 +0000 Subject: [PATCH] support for looking up existing species information svn path=/; revision=282 --- .../interactions/interactionPathsFromSif.pl | 8 ++- .../interactions/interactionTables.sql | 51 +++++++++++++++++++ .../athreyab/interactions/species_ncbi_list | 47 +++++++++++++++++ 3 files changed, 104 insertions(+), 2 deletions(-) create mode 100644 Personnel/athreyab/interactions/species_ncbi_list diff --git a/Personnel/athreyab/interactions/interactionPathsFromSif.pl b/Personnel/athreyab/interactions/interactionPathsFromSif.pl index da35aac..9e5b5bb 100644 --- a/Personnel/athreyab/interactions/interactionPathsFromSif.pl +++ b/Personnel/athreyab/interactions/interactionPathsFromSif.pl @@ -58,7 +58,7 @@ sub importParalogData my $entry = $_; # strip off newline characters - chomp $entry; + chomp $entry; $entry =~ s/\r//g; $entry =~ s/\n//g; @@ -221,13 +221,15 @@ switch($optionId){ #add a new species to our database. case "0" { + showAvailableSpecies(); addNewSpecies(getSpeciesProperties(1)); } #import ortholog information case "1" { print "\n\nYou are importing a file containing ortholog genes.\nMake sure you have information for both species\n"; - + + showAvailableSpecies(); print "Species - 1. Species to which gene ids in the first column belong to"; $speciesId1ForOrtholog = getSpeciesId(getSpeciesProperties(0)); #$speciesId1ForOrtholog ne "" || die "species not found in our tables.\n"; @@ -244,6 +246,7 @@ switch($optionId){ case "2" { print "\n\nYou are importing a file containing paralog genes.\nMake sure you have the species information"; + showAvailableSpecies(); $speciesIdForParalog = getSpeciesId(getSpeciesProperties(0)); $speciesIdForParalog ne "" || die ""; importParalogData(); @@ -252,6 +255,7 @@ switch($optionId){ { print "Make sure you have the following information:\n"; print "\tspecies to which the gene accessions in the .sif file belong to\n"; + showAvailableSpecies(); print "\tncbi id of the species\n"; $curatorId = getCuratorId(getCuratorProperties()); $speciesIdForSif = getSpeciesId(getSpeciesProperties(0)); diff --git a/Personnel/athreyab/interactions/interactionTables.sql b/Personnel/athreyab/interactions/interactionTables.sql index 594ad16..26b5b8a 100644 --- a/Personnel/athreyab/interactions/interactionTables.sql +++ b/Personnel/athreyab/interactions/interactionTables.sql @@ -415,6 +415,57 @@ INSERT INTO `Mode_of_action`(`mode_of_action`) VALUE('up regulates'); INSERT INTO `Mode_of_action`(`mode_of_action`) VALUE('down regulates'); +-- ----------------------------------------------------- +-- Populate `interaction`.`Species` with known values +-- ----------------------------------------------------- +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('59689','Arabidopsis lyrata'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('3702','Arabidopsis thaliana'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('15368','Brachypodium distachyon'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('6239','Caenorhabditis elegans'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('3649','Carica papaya'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('3055','Chlamydomonas reinhardtii'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('85681','Citrus clementina'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('2711','Citrus sinensis'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('3659','Cucumis sativus'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('7955','Danio rerio'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('7227','Drosophila melanogaster'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('2880','Ectocarpus siliculosus'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('562','Escherichia coli'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('71139','Eucalyptus grandis'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('57918','Fragaria vesca'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('5507','Fusarium oxysporum'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('3847','Glycine max'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('9606','Homo sapiens'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('180498','Jatropha curcas'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('29883','Laccaria bicolor'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('3983','Manihot esculenta'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('3880','Medicago truncatula'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('4155','Mimulus guttatus'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('10090','Mus musculus'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('140110','Nectria haematococca'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('5141','Neurospora crassa'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('272131','Nostoc punctiforme'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('4530','Oryza sativa'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('121225','Pediculus humanus'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('42345','Phoenix dactylifera'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('3218','Physcomitrella patens'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('3694','Populus trichocarpa'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('3760','Prunus persica'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('10116','Rattus norvegicus'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('64495','Rhizopus oryzae'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('3988','Ricinus communis'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('4932','Saccharomyces cerevisiae'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('4896','Schizosaccharomyces pombe'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('88036','Selaginella moellendorffii'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('4113','Solanum tuberosum'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('4558','Sorghum bicolor'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('3641','Theobroma cacao'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('29910','Tolypocladium inflatum'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('63577','Trichoderma atroviride'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('1206','Trichodesmium erythraeum'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('29760','Vitis vinifera'); +INSERT INTO `Species`(`NCBI_taxonomy_id`,`species`) VALUES('4577','Zea mays'); + SET SQL_MODE=@OLD_SQL_MODE; SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS; SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS; diff --git a/Personnel/athreyab/interactions/species_ncbi_list b/Personnel/athreyab/interactions/species_ncbi_list new file mode 100644 index 0000000..24df757 --- /dev/null +++ b/Personnel/athreyab/interactions/species_ncbi_list @@ -0,0 +1,47 @@ +59689 Arabidopsis lyrata +3702 Arabidopsis thaliana +15368 Brachypodium distachyon +6239 Caenorhabditis elegans +3649 Carica papaya +3055 Chlamydomonas reinhardtii +85681 Citrus clementina +2711 Citrus sinensis +3659 Cucumis sativus +7955 Danio rerio +7227 Drosophila melanogaster +2880 Ectocarpus siliculosus +562 Escherichia coli +71139 Eucalyptus grandis +57918 Fragaria vesca +5507 Fusarium oxysporum +3847 Glycine max +9606 Homo sapiens +180498 Jatropha curcas +29883 Laccaria bicolor +3983 Manihot esculenta +3880 Medicago truncatula +4155 Mimulus guttatus +10090 Mus musculus +140110 Nectria haematococca +5141 Neurospora crassa +272131 Nostoc punctiforme +4530 Oryza sativa +121225 Pediculus humanus +42345 Phoenix dactylifera +3218 Physcomitrella patens +3694 Populus trichocarpa +3760 Prunus persica +10116 Rattus norvegicus +64495 Rhizopus oryzae +3988 Ricinus communis +4932 Saccharomyces cerevisiae +4896 Schizosaccharomyces pombe +88036 Selaginella moellendorffii +4113 Solanum tuberosum +4558 Sorghum bicolor +3641 Theobroma cacao +29910 Tolypocladium inflatum +63577 Trichoderma atroviride +1206 Trichodesmium erythraeum +29760 Vitis vinifera +4577 Zea mays -- 2.34.1