Added species

svn path=/; revision=579

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index a0d37a98eea09b01265eb0de106ced017e9aa2c2..60df4700f8d488f0ae3f717586e3e6c752fe0a98 100755 (executable)
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -40,6 +40,8 @@ sub find_species {
                $species = "Cannabis_sativa.Purple.Kush";
        }elsif ($temp =~ /Capsella/) {
                $species = "Capsella_rubella";
+       }elsif ($temp =~ /Capsicum\_annuum/) {
+               $species = "Capsicum_annuum";
        }elsif ($temp =~ /Carica\_papaya/) {
                $species = "Carica_papaya";
        }elsif ($temp =~ /Chlamy/) {
@@ -136,6 +138,8 @@ sub find_species {
                $species = "Oryza_glumaepatula";
        }elsif ($temp =~ /Oryza\_granulata/) {
                $species = "Oryza_granulata";
+       }elsif ($temp =~ /Oryza\_kasalath/) {
+               $species = "Oryza_kasalath";
        }elsif ($temp =~ /Oryza\_longistaminata/) {
                $species = "Oryza_longistaminata";
        }elsif ($temp =~ /Oryza\_meridionalis/) {
@@ -154,6 +158,10 @@ sub find_species {
                $species = "Oryza_sativa.indica.gramene";
        }elsif ($temp =~ /Oryza\_sativa.indica\.iplant/) {
                $species = "Oryza_sativa.indica.iplant";
+       }elsif ($temp =~ /Oryza\_sativa.indica.IR29/) {
+               $species = "Oryza_sativa.indica.IR29";
+       }elsif ($temp =~ /Oryza\_sativa.indica.pokkali/) {
+               $species = "Oryza_sativa.indica.pokkali";
        }elsif ($temp =~ /Oryza\_sativa.japonica.IRGSP/) {
                $species = "Oryza_sativa.japonica.IRGSP";
        }elsif ($temp =~ /Oryza\_sativa.japonica.MSU/) {
@@ -277,6 +285,8 @@ sub find_gene {
        }elsif ($species eq "Capsella_rubella") {
                my ($gene_id, $transcript) = split(/\|/, $gene_header);
                $gene = $transcript;
+       }elsif ($species eq "Capsicum_annuum") {
+               $gene = $gene_header;
        }elsif ($species eq "Carica_papaya") {
                my ($contig,$gene_id) = split(/\|/, $gene_header);
                $gene = $gene_id;
@@ -428,6 +438,8 @@ sub find_gene {
        }elsif ($species eq "Oryza_granulata") {
                my ($gene_id, $strand, $start, $stop) = split(/\|/, $gene_header);
                $gene = $gene_id;
+       }elsif ($species eq "Oryza_kasalath") {
+               $gene = $gene_header;
        }elsif ($species eq "Oryza_longistaminata") {
                my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
                $gene = $gene_id;
@@ -456,6 +468,12 @@ sub find_gene {
                my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
         $transcript =~ s/transcript\://;
         $gene = $transcript;
+    }elsif ($species eq "Oryza_sativa.indica.IR29") {
+       my ($gene_id,$position, $start, $length) = split(/\|/, $gene_header);
+       $gene = $gene_id;
+    }elsif ($species eq "Oryza_sativa.indica.pokkali") {
+       my ($gene_id,$position, $start, $length) = split(/\|/, $gene_header);
+       $gene = $gene_id;
        }elsif ($species eq "Oryza_sativa.japonica.iplant") {
                my ($gene_id,$chrom,$program,$function,$type) = split(/[\|\s]+/, $gene_header);
                $gene = $gene_id;
@@ -862,6 +880,7 @@ sub all_species_array {
        push (@spec_array, "Cajanus_cajan");
        push (@spec_array, "Cannabis_sativa.Purple.Kush");
        push (@spec_array, "Capsella_rubella");
+       push (@spec_array, "Capsicum_annuum");
        push (@spec_array, "Carica_papaya");
        push (@spec_array, "Chlamydomonas_reinhardtii");
        push (@spec_array, "Cicer_arietinum");
@@ -909,6 +928,7 @@ sub all_species_array {
        push (@spec_array, "Oryza_glaberrima");
        push (@spec_array, "Oryza_glumaepatula");
        push (@spec_array, "Oryza_granulata");
+       push (@spec_array, "Oryza_kasalath");
        push (@spec_array, "Oryza_longistaminata");
        push (@spec_array, "Oryza_meridionalis");
        push (@spec_array, "Oryza_minuta");
@@ -918,6 +938,8 @@ sub all_species_array {
        push (@spec_array, "Oryza_rufipogon");
        push (@spec_array, "Oryza_sativa.indica.gramene");
        push (@spec_array, "Oryza_sativa.indica.iplant");
+       push (@spec_array, "Oryza_sativa.indica.IR29");
+       push (@spec_array, "Oryza_sativa.indica.pokkali");
        push (@spec_array, "Oryza_sativa.japonica.iplant");
        push (@spec_array, "Oryza_sativa.japonica.IRGSP");
        push (@spec_array, "Oryza_sativa.japonica.MSU");