support for looking up existing species information

svn path=/; revision=282

diff --git a/Personnel/athreyab/interactions/interactionPathsFromSif.pl b/Personnel/athreyab/interactions/interactionPathsFromSif.pl
index da35aac2191ba10af3efc74e1e2594c7604e0771..9e5b5bb0998994d87838ad95379aecf7249a9c71 100644 (file)
--- 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 594ad161c5d392303ade9505d320d62e9469ff8b..26b5b8ac20d3a0810a86849f659b7b321e048eed 100644 (file)
--- 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 (file)
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