From 9d5f4971ee880f285b5bd3e90bafa234caad370f Mon Sep 17 00:00:00 2001 From: elserj Date: Mon, 16 Feb 2015 21:34:34 +0000 Subject: [PATCH] Fix incorrect C.elegans gene names svn path=/; revision=604 --- interactome_scripts/find_species.pl | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) 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; -- 2.34.1