Update for new fasta files

svn path=/; revision=118

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 8b9bb6b99090a07a9684ff674938f7ae22467883..a3f9be66abf3ccf743124dc2bd88fbe3e2f2f68a 100755 (executable)
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -226,7 +226,7 @@ sub find_gene {
                $gene = $gene_id;
        }elsif ($species eq "Nostoc_punctiforme") {
                my ($temp,$transcript,$source,$gene_id,$func) = split(/\|/, $gene_header);
-               $gene = $gene_id;
+               $gene = $transcript;
        }elsif ($species eq "Oryza_sativa") {
                my ($isomer,$temp,$type) = split(/\|/,$gene_header);
                $gene = $isomer;
@@ -241,8 +241,8 @@ sub find_gene {
                my ($name,$locus_id,$scaffold,$prot_id) = split(/\|/,$gene_header);
                $gene = $prot_id; #???
        }elsif ($species eq "Populus_trichocarpa") {
-               my ($name,$gene_id,$scaffold,$prot_id) = split(/\|/,$gene_header);
-               $gene = $gene_id; #???
+               my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
+               $gene = $transcript_id;
        }elsif ($species eq "Prunus_persica") {
                my ($gene_id,$temp) = split(/\s/,$gene_header);
                $gene = $gene_id;
@@ -265,8 +265,8 @@ sub find_gene {
                my ($name,$locus_id,$chrom_id,$prot_id) = split(/\|/,$gene_header);
                $gene = $prot_id; #???
        }elsif ($species eq "Sorghum_bicolor") {
-               my ($name,$gene_id,$chrom,$prot_id) = split(/\|/,$gene_header);
-               $gene = $gene_id; #???
+               my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
+               $gene = $transcript_id;
        }elsif ($species eq "Synechocystis_pcc6803") {
                my ($gene_id,$temp) = split(" ",$gene_header);
                $gene = $gene_id; #???
@@ -289,8 +289,8 @@ sub find_gene {
                my ($temp,$unknown,$source,$gene_id,$func) = split(/\|/, $gene_header);
                $gene = $gene_id;
        }elsif ($species eq "Vitis_vinifera") {
-               my ($name,$gene_id,$chrom_id,$id) = split(/\|/,$gene_header);
-               $gene = $gene_id; #???
+               #my ($name,$gene_id,$chrom_id,$id) = split(/\|/,$gene_header);
+               $gene = $gene_header; #???
        }elsif ($species eq "Zea_mays") {
                my ($transcript,$seq_type,$coord,$parent_transcript,$parent_gene) = split(/;\s/, $gene_header);
                $gene = $transcript;