Added new bean species, Arachis_duramensis, Arachis_ipaensis, Phaseolus_vulgaris

svn path=/; revision=635

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index e6cd283a697f0f8e1639b07e97614ac2e767f1b8..6b9fc70d0a06762950da29a1fd6ba0bbc1216085 100755 (executable)
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -20,6 +20,10 @@ sub find_species {
                $species = "Arabidopsis_lyrata";
        }elsif ($temp =~ /Arabidopsis\_thaliana/) {
                $species = "Arabidopsis_thaliana";
+       }elsif ($temp =~ /Arachis\_duramensis/) {
+               $species = "Arachis_duramensis";
+       }elsif ($temp =~ /Arachis\_ipaensis/) {
+               $species = "Arachis_ipaensis";
        }elsif ($temp =~ /Batrachochytrium/) {
                $species = "Batrachochytrium_dendrobatidis";
        }elsif ($temp =~ /Brachypodium\_distachyon/) {
@@ -178,6 +182,8 @@ sub find_species {
                $species = "Oryzias\_latipes";
        }elsif ($temp =~ /Pediculus/) {
                $species = "Pediculus_humanus";
+       }elsif ($temp =~ /Phaseolus\_vulgaris/) {
+               $species = "Phaseolus_vulgaris";
        }elsif ($temp =~ /Phoenix/) {
                $species = "Phoenix_dactylifera";
        }elsif ($temp =~ /Phyllostachys/) {
@@ -264,6 +270,12 @@ sub find_gene {
        }elsif ($species eq "Arabidopsis_thaliana") {
                my ($gene_id,$isomer) = split(/\|/, $gene_header);
                $gene = $isomer;
+       }elsif ($species eq "Arachis_duramensis") {
+               my ($gene_id, $desc) = split(/\s/, $gene_header);
+               $gene = $gene_id;
+       }elsif ($species eq "Arachis_ipaensis") {
+               my ($gene_id, $desc) = split(/\s/, $gene_header);
+               $gene = $gene_id;
        }elsif ($species eq "Batrachochytrium_dendrobatidis") {
                my ($transcript,$gene_id,$info) = split(/\s\|\s/, $gene_header);
                $gene = $transcript;
@@ -506,6 +518,9 @@ sub find_gene {
                my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
             $transcript =~ s/transcript\://;
             $gene = $transcript;
+    }elsif ($species eq "Phaseolus_vulgaris") {
+       my ($gene_id, $transcript) = split(/\|/,$gene_header);
+       $gene = $transcript;
        }elsif ($species eq "Pediculus_humanus") {
                my ($gene_pa,$func,$func2,$unknown,$gene_id) = split(/[\|\s+]/, $gene_header);
                $gene = $gene_pa;
@@ -797,6 +812,9 @@ sub find_gene_synonym {
                my ($gene_pa,$func,$func2,$unknown,$gene_id) = split(/[\|\s+]/, $gene_header);
                $gene_id =~ s/gene\://;
                $synonym = $gene_id;
+       }elsif ($species eq "Phaseolus_vulgaris") {
+               my ($gene_id, $transcript) = split(/\|/,$gene_header);
+               $synonym = $gene_id;
        }elsif ($species eq "Phoenix_dactylifera") {
                my ($gene_id, $locus_tag, $product, $strand) = split(/\s\[/, $gene_header);
                $locus_tag =~ s/locus_tag=//;
@@ -909,6 +927,8 @@ sub all_species_array {
        push (@spec_array, "Amborella_trichopoda");
        push (@spec_array, "Arabidopsis_lyrata");
        push (@spec_array, "Arabidopsis_thaliana");
+       push (@spec_array, "Arachis_duramensis");
+       push (@spec_array, "Arachis_ipaensis");
        push (@spec_array, "Batrachochytrium_dendrobatidis");
        push (@spec_array, "Brachypodium_distachyon");
        push (@spec_array, "Brachypodium_sylvaticum_Corvallis");
@@ -987,6 +1007,7 @@ sub all_species_array {
        push (@spec_array, "Oryza_sativa.japonica.MSU");
        push (@spec_array, "Oryzias_latipes");
        push (@spec_array, "Pediculus_humanus");
+       push (@spec_array, "Phaseolus_vulgaris");
        push (@spec_array, "Phyllostachys_heterocycla");
        push (@spec_array, "Physcomitrella_patens");
        push (@spec_array, "Phytophthora_infestans");