From f35dd3ad00b426e63f944d22e9c7c1dc1faf0115 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Tue, 20 Oct 2015 22:21:09 +0000
Subject: [PATCH] Fix spelling of Arachis duranensis and add two Salvia species
 for Matt

svn path=/; revision=637
---
 interactome_scripts/find_species.pl | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 6b9fc70..47ea499 100755
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -20,8 +20,8 @@ sub find_species {
 		$species = "Arabidopsis_lyrata";
 	}elsif ($temp =~ /Arabidopsis\_thaliana/) {
 		$species = "Arabidopsis_thaliana";
-	}elsif ($temp =~ /Arachis\_duramensis/) {
-		$species = "Arachis_duramensis";
+	}elsif ($temp =~ /Arachis\_duranensis/) {
+		$species = "Arachis_duranensis";
 	}elsif ($temp =~ /Arachis\_ipaensis/) {
 		$species = "Arachis_ipaensis";
 	}elsif ($temp =~ /Batrachochytrium/) {
@@ -210,6 +210,10 @@ sub find_species {
 		$species = "Ricinus_communis";
 	}elsif ($temp =~ /cerevisiae/) {
 		$species = "Saccharomyces_cerevisiae";
+	}elsif ($temp =~ /Salvia_hispancia\.salba/) {
+		$species = "Salvia_hispancia.salba";
+	}elsif ($temp =~ /Salvia_splendens/) {
+		$species = "Salvia_splendens";
 	}elsif ($temp =~ /pombe/) {
 		$species = "Schizosaccharomyces_pombe";
 	}elsif ($temp =~ /Selaginella/) {
@@ -270,7 +274,7 @@ sub find_gene {
 	}elsif ($species eq "Arabidopsis_thaliana") {
 		my ($gene_id,$isomer) = split(/\|/, $gene_header);
 		$gene = $isomer;
-	}elsif ($species eq "Arachis_duramensis") {
+	}elsif ($species eq "Arachis_duranensis") {
 		my ($gene_id, $desc) = split(/\s/, $gene_header);
 		$gene = $gene_id;
 	}elsif ($species eq "Arachis_ipaensis") {
@@ -565,6 +569,10 @@ 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 "Salvia_hispancia.salba") {
+    	$gene = $gene_header;
+    }elsif ($species eq "Salvia_splendens") {
+    	$gene = $gene_header;
 	}elsif ($species eq "Schizosaccharomyces_pombe") {
 		my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
         $transcript =~ s/transcript\://;
@@ -927,7 +935,7 @@ 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_duranensis");
 	push (@spec_array, "Arachis_ipaensis");
 	push (@spec_array, "Batrachochytrium_dendrobatidis");
 	push (@spec_array, "Brachypodium_distachyon");
@@ -1018,6 +1026,8 @@ sub all_species_array {
 	push (@spec_array, "Rhizopus_oryzae");
 	push (@spec_array, "Ricinus_communis");
 	push (@spec_array, "Saccharomyces_cerevisiae");
+	push (@spec_array, "Salvia_hispancia.salba");
+	push (@spec_array, "Salvia_splendens");
 	push (@spec_array, "Schizosaccharomyces_pombe");
 	push (@spec_array, "Selaginella_moellendorffii");
 	push (@spec_array, "Setaria_italica");
-- 
2.34.1