From 6aae0e163c8e16ccdfbb9da2f7660051048b7517 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Tue, 22 Jul 2014 22:42:49 +0000
Subject: [PATCH] Added species

svn path=/; revision=579
---
 interactome_scripts/find_species.pl | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index a0d37a9..60df470 100755
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -40,6 +40,8 @@ sub find_species {
 		$species = "Cannabis_sativa.Purple.Kush";
 	}elsif ($temp =~ /Capsella/) {
 		$species = "Capsella_rubella";
+	}elsif ($temp =~ /Capsicum\_annuum/) {
+		$species = "Capsicum_annuum";
 	}elsif ($temp =~ /Carica\_papaya/) {
 		$species = "Carica_papaya";
 	}elsif ($temp =~ /Chlamy/) {
@@ -136,6 +138,8 @@ sub find_species {
 		$species = "Oryza_glumaepatula";
 	}elsif ($temp =~ /Oryza\_granulata/) {
 		$species = "Oryza_granulata";
+	}elsif ($temp =~ /Oryza\_kasalath/) {
+		$species = "Oryza_kasalath";
 	}elsif ($temp =~ /Oryza\_longistaminata/) {
 		$species = "Oryza_longistaminata";
 	}elsif ($temp =~ /Oryza\_meridionalis/) {
@@ -154,6 +158,10 @@ sub find_species {
 		$species = "Oryza_sativa.indica.gramene";
 	}elsif ($temp =~ /Oryza\_sativa.indica\.iplant/) {
 		$species = "Oryza_sativa.indica.iplant";
+	}elsif ($temp =~ /Oryza\_sativa.indica.IR29/) {
+		$species = "Oryza_sativa.indica.IR29";
+	}elsif ($temp =~ /Oryza\_sativa.indica.pokkali/) {
+		$species = "Oryza_sativa.indica.pokkali";
 	}elsif ($temp =~ /Oryza\_sativa.japonica.IRGSP/) {
 		$species = "Oryza_sativa.japonica.IRGSP";
 	}elsif ($temp =~ /Oryza\_sativa.japonica.MSU/) {
@@ -277,6 +285,8 @@ sub find_gene {
 	}elsif ($species eq "Capsella_rubella") {
 		my ($gene_id, $transcript) = split(/\|/, $gene_header);
 		$gene = $transcript;
+	}elsif ($species eq "Capsicum_annuum") {
+		$gene = $gene_header;
 	}elsif ($species eq "Carica_papaya") {
 		my ($contig,$gene_id) = split(/\|/, $gene_header);
 		$gene = $gene_id;
@@ -428,6 +438,8 @@ sub find_gene {
 	}elsif ($species eq "Oryza_granulata") {
 		my ($gene_id, $strand, $start, $stop) = split(/\|/, $gene_header);
 		$gene = $gene_id;
+	}elsif ($species eq "Oryza_kasalath") {
+		$gene = $gene_header;
 	}elsif ($species eq "Oryza_longistaminata") {
 		my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
 		$gene = $gene_id;
@@ -456,6 +468,12 @@ sub find_gene {
 		my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
         $transcript =~ s/transcript\://;
         $gene = $transcript;
+    }elsif ($species eq "Oryza_sativa.indica.IR29") {
+    	my ($gene_id,$position, $start, $length) = split(/\|/, $gene_header);
+    	$gene = $gene_id;
+    }elsif ($species eq "Oryza_sativa.indica.pokkali") {
+    	my ($gene_id,$position, $start, $length) = split(/\|/, $gene_header);
+    	$gene = $gene_id;
 	}elsif ($species eq "Oryza_sativa.japonica.iplant") {
 		my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
 		$gene = $gene_id;
@@ -862,6 +880,7 @@ sub all_species_array {
 	push (@spec_array, "Cajanus_cajan");
 	push (@spec_array, "Cannabis_sativa.Purple.Kush");
 	push (@spec_array, "Capsella_rubella");
+	push (@spec_array, "Capsicum_annuum");
 	push (@spec_array, "Carica_papaya");
 	push (@spec_array, "Chlamydomonas_reinhardtii");
 	push (@spec_array, "Cicer_arietinum");
@@ -909,6 +928,7 @@ sub all_species_array {
 	push (@spec_array, "Oryza_glaberrima");
 	push (@spec_array, "Oryza_glumaepatula");
 	push (@spec_array, "Oryza_granulata");
+	push (@spec_array, "Oryza_kasalath");
 	push (@spec_array, "Oryza_longistaminata");
 	push (@spec_array, "Oryza_meridionalis");
 	push (@spec_array, "Oryza_minuta");
@@ -918,6 +938,8 @@ sub all_species_array {
 	push (@spec_array, "Oryza_rufipogon");
 	push (@spec_array, "Oryza_sativa.indica.gramene");
 	push (@spec_array, "Oryza_sativa.indica.iplant");
+	push (@spec_array, "Oryza_sativa.indica.IR29");
+	push (@spec_array, "Oryza_sativa.indica.pokkali");
 	push (@spec_array, "Oryza_sativa.japonica.iplant");
 	push (@spec_array, "Oryza_sativa.japonica.IRGSP");
 	push (@spec_array, "Oryza_sativa.japonica.MSU");
-- 
2.34.1