From eaa6f8a8c01b9ccfc82da4d3c2a66d86c55813a7 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Sat, 9 Jul 2011 00:44:57 +0000
Subject: [PATCH] Update for new fasta files

svn path=/; revision=118
---
 interactome_scripts/find_species.pl | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 8b9bb6b..a3f9be6 100755
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -226,7 +226,7 @@ sub find_gene {
 		$gene = $gene_id;
 	}elsif ($species eq "Nostoc_punctiforme") {
 		my ($temp,$transcript,$source,$gene_id,$func) = split(/\|/, $gene_header);
-		$gene = $gene_id;
+		$gene = $transcript;
 	}elsif ($species eq "Oryza_sativa") {
 		my ($isomer,$temp,$type) = split(/\|/,$gene_header);
 		$gene = $isomer;
@@ -241,8 +241,8 @@ sub find_gene {
 		my ($name,$locus_id,$scaffold,$prot_id) = split(/\|/,$gene_header);
 		$gene = $prot_id; #???
 	}elsif ($species eq "Populus_trichocarpa") {
-		my ($name,$gene_id,$scaffold,$prot_id) = split(/\|/,$gene_header);
-		$gene = $gene_id; #???
+		my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
+		$gene = $transcript_id;
 	}elsif ($species eq "Prunus_persica") {
 		my ($gene_id,$temp) = split(/\s/,$gene_header);
 		$gene = $gene_id;
@@ -265,8 +265,8 @@ sub find_gene {
 		my ($name,$locus_id,$chrom_id,$prot_id) = split(/\|/,$gene_header);
 		$gene = $prot_id; #???
 	}elsif ($species eq "Sorghum_bicolor") {
-		my ($name,$gene_id,$chrom,$prot_id) = split(/\|/,$gene_header);
-		$gene = $gene_id; #???
+		my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
+		$gene = $transcript_id;
 	}elsif ($species eq "Synechocystis_pcc6803") {
 		my ($gene_id,$temp) = split(" ",$gene_header);
 		$gene = $gene_id; #???
@@ -289,8 +289,8 @@ sub find_gene {
 		my ($temp,$unknown,$source,$gene_id,$func) = split(/\|/, $gene_header);
 		$gene = $gene_id;
 	}elsif ($species eq "Vitis_vinifera") {
-		my ($name,$gene_id,$chrom_id,$id) = split(/\|/,$gene_header);
-		$gene = $gene_id; #???
+		#my ($name,$gene_id,$chrom_id,$id) = split(/\|/,$gene_header);
+		$gene = $gene_header; #???
 	}elsif ($species eq "Zea_mays") {
 		my ($transcript,$seq_type,$coord,$parent_transcript,$parent_gene) = split(/;\s/, $gene_header);
 		$gene = $transcript;
-- 
2.34.1