From 03bf5c9fc11065abb0cbb6aac3a838b7706129ee Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Sat, 15 Feb 2014 00:23:51 +0000
Subject: [PATCH] Added 4 new Oryza species from Pankaj

svn path=/; revision=528
---
 interactome_scripts/find_species.pl | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index c93b9fa..1f9ea86 100755
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -116,6 +116,8 @@ sub find_species {
 		$species = "Nostoc_punctiforme";
 	}elsif ($temp =~ /Oncorhynchus\_mykiss/) {
 		$species = "Oncorhynchus\_mykiss";
+	}elsif ($temp =~ /Oryza\_australiensis/) {
+		$species = "Oryza_australiensis";
 	}elsif ($temp =~ /Oryza\_barthii/) {
 		$species = "Oryza_barthii";
 	}elsif ($temp =~ /Oryza\_brachyantha/) {
@@ -124,12 +126,18 @@ sub find_species {
 		$species = "Oryza_glaberrima";
 	}elsif ($temp =~ /Oryza\_glumaepatula/) {
 		$species = "Oryza_glumaepatula";
+	}elsif ($temp =~ /Oryza\_granulata/) {
+		$species = "Oryza_granulata";
 	}elsif ($temp =~ /Oryza\_longistaminata/) {
 		$species = "Oryza_longistaminata";
 	}elsif ($temp =~ /Oryza\_meridionalis/) {
 		$species = "Oryza_meridionalis";
+	}elsif ($temp =~ /Oryza\_minuta/) {
+		$species = "Oryza_minuta";
 	}elsif ($temp =~ /Oryza\_nivara/) {
 		$species = "Oryza_nivara";
+	}elsif ($temp =~ /Oryza\_officinalis/) {
+		$species = "Oryza_officinalis";
 	}elsif ($temp =~ /Oryza\_punctata/) {
 		$species = "Oryza_punctata";
 	}elsif ($temp =~ /Oryza\_rufipogon/) {
@@ -380,6 +388,9 @@ sub find_gene {
 	}elsif ($species eq "Leersia_perrieri") {
 		my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
 		$gene = $gene_id;
+	}elsif ($species eq "Oryza_australiensis") {
+		my ($gene_id, $strand, $start, $stop) = split(/\|/, $gene_header);
+		$gene = $gene_id;
 	}elsif ($species eq "Oryza_barthii") {
 		my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
 		$gene = $gene_id;
@@ -392,15 +403,24 @@ sub find_gene {
 	}elsif ($species eq "Oryza_glumaepatula") {
 		my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
 		$gene = $gene_id;
+	}elsif ($species eq "Oryza_granulata") {
+		my ($gene_id, $strand, $start, $stop) = split(/\|/, $gene_header);
+		$gene = $gene_id;
 	}elsif ($species eq "Oryza_longistaminata") {
 		my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
 		$gene = $gene_id;
 	}elsif ($species eq "Oryza_meridionalis") {
 		my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
 		$gene = $gene_id;
+	}elsif ($species eq "Oryza_minuta") {
+		my ($gene_id, $strand, $start, $stop) = split(/\|/, $gene_header);
+		$gene = $gene_id;
 	}elsif ($species eq "Oryza_nivara") {
 		my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
 		$gene = $gene_id;
+	}elsif ($species eq "Oryza_officinalis") {
+		my ($gene_id, $strand, $start, $stop) = split(/\|/, $gene_header);
+		$gene = $gene_id;
 	}elsif ($species eq "Oryza_punctata") {
 		my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
 		$gene = $gene_id;
@@ -849,13 +869,17 @@ sub all_species_array {
 	push (@spec_array, "Neurospora_crassa");
 	push (@spec_array, "Nostoc_punctiforme");
 	push (@spec_array, "Oncorhynchus_mykiss");
+	push (@spec_array, "Oryza_australiensis");
 	push (@spec_array, "Oryza_barthii");
 	push (@spec_array, "Oryza_brachyantha");
 	push (@spec_array, "Oryza_glaberrima");
 	push (@spec_array, "Oryza_glumaepatula");
+	push (@spec_array, "Oryza_granulata");
 	push (@spec_array, "Oryza_longistaminata");
 	push (@spec_array, "Oryza_meridionalis");
+	push (@spec_array, "Oryza_minuta");
 	push (@spec_array, "Oryza_nivara");
+	push (@spec_array, "Oryza_officinalis");
 	push (@spec_array, "Oryza_punctata");
 	push (@spec_array, "Oryza_rufipogon");
 	push (@spec_array, "Oryza_sativa.indica.gramene");
-- 
2.34.1