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 3199535008c851b182d00b01e41c2cc16b0c8945..8c9c93e63ad33af9dd321d9e89b1784b27e913b1 100755 (executable)
--- 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;