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 d357d1b3579386baefb998ce6099e6d16e74c3df..b12de4e08a002fa81a1a9f074b4154dfaba8ffa0 100755 (executable)
--- 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\://;