Add citrus, eucalyptus and apple to gene detection

svn path=/; revision=84

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 579482f5a5fb2942efdd3b2062da575a8787c946..8e83af3d1311184b7eefc152df2431d1e603c02f 100755 (executable)
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -22,6 +22,10 @@ sub find_species {
                $temp = "Carica_papaya";
        }elsif ($temp =~ /Chlamy/) {
                $temp = "Chlamydomonas_reinhardtii";
+       }elsif ($temp =~ /Citrus\_clementina/) {
+               $temp = "Citrus_clementina";
+       }elsif ($temp =~ /Citrus\_sinensis/) {
+               $temp = "Citrus_sinensis";
        }elsif ($temp =~ /Cucumis\_sativus/) {
                $temp = "Cucumis_sativus";
        }elsif ($temp =~ /Danio/) {
@@ -34,6 +38,8 @@ sub find_species {
                $temp = "Epichloe\_festuca";
        }elsif ($temp =~ /Escherichia\_coli/) {
                $temp = "Escherichia_coli";
+       }elsif ($temp =~ /Eucalyptus\_grandis/) {
+               $temp = "Eucalyptus_grandis";
        }elsif ($temp =~ /Fragaria/) {
                $temp = "Fragaria_vesca";
        }elsif ($temp =~ /Fusarium_graminearum/) {
@@ -50,6 +56,8 @@ sub find_species {
                $temp = "Laccaria_bicolor";
        }elsif ($temp =~ /Magnaporthe/) {
                $temp = "Magnaporthe_grissa";
+       }elsif ($temp =~ /Malus/) {
+               $temp = "Malus_domestica";
        }elsif ($temp =~ /Manihot/) {
                $temp = "Manihot_esculenta";
        }elsif ($temp =~ /Medicago/) {
@@ -136,6 +144,12 @@ sub find_gene {
        }elsif ($species eq "Chlamydomonas_reinhardtii") {
                my ($name,$locus_id,$chrom,$transcript) = split(/\|/,$gene_header);
                $gene = $transcript; #???
+       }elsif ($species eq "Citrus_clementina") {
+               my ($gene_id,$pacid) = split(/\|/,$gene_header);
+               $gene = $gene_id;
+       }elsif ($species eq "Citrus_sinensis") {
+               my ($gene_id,$pacid) = split(/\|/,$gene_header);
+               $gene = $gene_id;
        }elsif ($species eq "Cucumis_sativus") {
                my ($name,$main_isomer,$scaffold,$isomer) = split(/\|/,$gene_header);
                $gene = $isomer;
@@ -152,6 +166,9 @@ sub find_gene {
                $gene = $gene_header;
        }elsif ($species eq "Escherichia_coli") {
                $gene = $gene_header; #???
+       }elsif ($species eq "Eucalyptus_grandis") {
+               my ($gene_id,$pacid) = split(/\|/,$gene_header);
+               $gene = $gene_id;
        }elsif ($species eq "Fragaria_vesca") {
                my ($gene_id, $mrna_id, $method, $length) = split(/\s\|\s/, $gene_header);
                $gene = $gene_id;
@@ -175,6 +192,8 @@ sub find_gene {
        }elsif ($species eq "Magnaporthe_grissa") {
                my ($transcript,$gene_id,$temp) = split(/\s\|\s/, $gene_header);
                $gene = $transcript;
+       }elsif ($species eq "Malus_domestica" ) {
+               $gene = $gene_header;
        }elsif ($species eq "Manihot_esculenta") {
                my ($name,$scaffold,$gene_id,$temp) = split(/\|/, $gene_header);
                $gene = $gene_id;