From: elserj <elserj@localhost>
Date: Mon, 16 Feb 2015 21:34:34 +0000 (+0000)
Subject: Fix incorrect C.elegans gene names
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=9d5f4971ee880f285b5bd3e90bafa234caad370f;p=old-jaiswallab-svn%2F.git

Fix incorrect C.elegans gene names

svn path=/; revision=604
---

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 3199535..8c9c93e 100755
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -283,8 +283,9 @@ sub find_gene {
 		my ($gene_id,$transcript) = split(/\|/, $gene_header);
 		$gene = $transcript; #????
 	}elsif ($species eq "Caenorhabditis_elegans") {
-		my ($locus_id,$unknown,$gene_id,$temp) = split(/\|/, $gene_header);
-		$gene = $locus_id; #???
+		my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
+		$transcript =~ s/transcript\://;
+		$gene = $transcript;
 	}elsif ($species eq "Cajanus_cajan") {
 		my ($gene_id,$type,$locus,$temp) = split(/\s/, $gene_header);
 		$gene = $gene_id;
@@ -630,8 +631,11 @@ sub find_gene_synonym {
 		$peptide =~ s/\:pep//;
 		$synonym = "$peptide,$gene_id";
 	}elsif ($species eq "Caenorhabditis_elegans") {
-		my ($locus_id,$unknown,$gene_id,$temp) = split(/\|/, $gene_header);
-		$synonym = $gene_id; #???
+		my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
+		$transcript =~ s/transcript\://;
+		$gene_id =~ s/gene\://;
+		$peptide =~ s/\:pep//;
+		$synonym = "$peptide,$gene_id";
 	}elsif ($species eq "Cajanus_cajan") {
 		my ($gene_id,$type,$locus,$temp) = split(/\s/, $gene_header);
 		$synonym = $locus;