From: elserj <elserj@localhost>
Date: Thu, 8 Oct 2015 21:55:39 +0000 (+0000)
Subject: Added new bean species, Arachis_duramensis, Arachis_ipaensis, Phaseolus_vulgaris
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=d92f71f596125eae6cced4c66481d6f30eaefa85;p=old-jaiswallab-svn%2F.git

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 e6cd283..6b9fc70 100755
--- 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");