From: elserj <elserj@localhost>
Date: Mon, 16 Feb 2015 22:24:22 +0000 (+0000)
Subject: Fix a couple more incorrect gene names
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=c52ce294b5c330d9ec7c6ed9cd9390e459552e89;p=old-jaiswallab-svn%2F.git

Fix a couple more incorrect gene names

svn path=/; revision=606
---

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index d357d1b..b12de4e 100755
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -508,7 +508,7 @@ sub find_gene {
 		my ($gene_id, $locus_tag, $product, $strand) = split(/\s\[/, $gene_header);
 		$gene = $gene_id;
 	}elsif ($species eq "Phyllostachys_heterocycla") {
-		my ($gene_id, $gene_model, $location, $dot, $strand, $dot2, $info) = split (/\s+/, $gene_header);
+		my ($gene_id, $gene_model, $location, $dot, $strand, $dot2, $info) = split (/\|/, $gene_header);
 		$gene = $gene_id;
 	}elsif ($species eq "Physcomitrella_patens") {
 		my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
@@ -791,9 +791,6 @@ sub find_gene_synonym {
 		$locus_tag =~ s/locus_tag=//;
 		$locus_tag =~ s/"//g;
 		$synonym = $locus_tag;
-	}elsif ($species eq "Phyllostachys_heterocycla") {
-		my ($gene_id, $gene_model, $location, $dot, $strand, $dot2, $info) = split (/\s+/, $gene_header);
-		$gene = $gene_id;
 	}elsif ($species eq "Physcomitrella_patens") {
 		my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
 		$synonym = $gene_id;
@@ -861,8 +858,11 @@ sub find_gene_synonym {
 		my ($gene_id,$transcript) = split(/\s/,$gene_header);
 		$synonym = $transcript;
 	}elsif ($species eq "Trichodesmium_erythraeum") {
-		my ($temp,$unknown,$source,$gene_id,$func) = split(/\|/, $gene_header);
-		$gene = $gene_id;
+		my ($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 "Triticum_aestivum") {
 		my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
         $transcript =~ s/transcript\://;