Added subroutine to only add the gene or locus id to db instead of entire gene header...

svn path=/; revision=10

diff --git a/interactome_scripts/inparanoid_output_parse.pl b/interactome_scripts/inparanoid_output_parse.pl
index 5864f8cf70bff672dea975e77ffe8d13cf2474c0..3528d9738bbaa168eb4fc6c1ed0e8d4bddc6fecd 100755 (executable)
--- a/interactome_scripts/inparanoid_output_parse.pl
+++ b/interactome_scripts/inparanoid_output_parse.pl
@@ -104,7 +104,8 @@ foreach my $input_file (@files) {
                        $id = $id_hash{$clust_id};
                }
        
-               $sth->execute($id, $bit_score, $species, $score, $gene_header);
+               my $gene = find_gene($gene_header,$species);
+               $sth->execute($id, $bit_score, $species, $score, $gene);
        
                $clust_id_prev = $clust_id;
 
@@ -165,4 +166,67 @@ sub find_species {
        return $temp;
 }
 
+sub find_gene {
+       my $gene_header = $_[0];
+       my $species = $_[1];
+       my $gene;
+       if ($species eq "Ath") {
+               my ($name,$gene_id,$chrom,$isomer) = split("\|", $gene_header);
+               $gene = $isomer;
+       }elsif ($species eq "Brachy") {
+               $gene = $gene_header;
+       }elsif ($species eq "C_elegans") {
+               my ($gene_id,$temp) = split("\|", $gene_header);
+               $gene = $gene_id; #???
+       }elsif ($species eq "Chlamy") {
+               my ($name,$locus_id,$scaff_id,$temp) = split("\|",$gene_header);
+               $gene = $locus_id; #???
+       }elsif ($species eq "Danio") {
+               $gene = $gene_header;
+       }elsif ($species eq "E_coli") {
+               $gene = $gene_header; #???
+       }elsif ($species eq "Soy") {
+               my ($name,$locus_id,$scaff_id,$isomer) = split("\|",$gene_header);
+               $gene = $isomer;
+       }elsif ($species eq "Human") {
+               $gene = $gene_header;
+       }elsif ($species eq "Maize") {
+               $gene = $gene_header;
+       }elsif ($species eq "Mouse") {
+               $gene = $gene_header;
+       }elsif ($species eq "Neurospora") {
+               $gene = $gene_header;
+       }elsif ($species eq "Oryza_sativa") {
+               my ($isomer,$temp,$type) = split("\|",$gene_header);
+               $gene = $isomer;
+       }elsif ($species eq "Physcomitreall") {
+               my ($name,$locus_id,$chrom_id,$prot_id) = split("\|",$gene_header);
+               $gene = $prot_id; #???
+       }elsif ($species eq "Poplar") {
+               my ($name,$locus_id,$chrom_id,$prot_id) = split("\|",$gene_header);
+               $gene = $prot_id; #???
+       }elsif ($species eq "Sacc_cerevisiae") {
+               $gene = $gene_header;
+       }elsif ($species eq "Sacc_pombe") {
+               $gene = $gene_header;
+       }elsif ($species eq "Selaginella") {
+               my ($name,$locus_id,$chrom_id,$prot_id) = split("\|",$gene_header);
+               $gene = $prot_id; #???
+       }elsif ($species eq "Sorghum") {
+               my ($name,$locus_id,$scaff_id,$prot_id) = split("\|",$gene_header);
+               $gene = $prot_id; #???
+       }elsif ($species eq "Synechosystis") {
+               my ($gene_id,$type,$temp) = split(" ",$gene_header);
+               $gene = $gene_id; #???
+       }elsif ($species eq "Grape") {
+               my ($name,$gene_id,$chrom_id,$id) = split("\|",$gene_header);
+               $gene = $gene_id; #???
+       }else {
+               die "Error: Gene id can not be found!";
+       }
+       return $gene;
+}
+               
+               
+