Added new fish species

svn path=/; revision=480

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 4f78afd9cf43e760b289ce465912382cc68332c9..b532dd9b00310e64f969a5f0eefc6803a36dcda5 100755 (executable)
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -11,7 +11,9 @@
 
 sub find_species {
        my $temp = $_[0];
-       if ($temp =~ /Arabidopsis\_lyrata/) {
+       if ($temp =~ /Aegilops\_tauschii/) {
+               $temp = "Aegilops_tauschii";
+       }elsif ($temp =~ /Arabidopsis\_lyrata/) {
                $temp = "Arabidopsis_lyrata";
        }elsif ($temp =~ /Arabidopsis\_thaliana/) {
                $temp = "Arabidopsis_thaliana";
@@ -51,10 +53,16 @@ sub find_species {
                $temp = "Fusarium\_oxysporum";
        }elsif ($temp =~ /Fusarium_verticilliodes/) {
                $temp = "Fusarium\_verticilliodes";
+       }elsif ($temp =~ /Gadus_morhua/) {
+               $temp = "Gadus\_morhua";
+       }elsif ($temp =~ /Gastroerosteus/) {
+               $temp = "Gastroerosteus\_aculeatus";
        }elsif ($temp =~ /Glycine/) {
                $temp = "Glycine_max";
        }elsif ($temp =~ /Homo\_sapiens/) {
                $temp = "Homo_sapiens";
+       }elsif ($temp =~ /Hordeum\_vulgare/) {
+               $temp = "Hordeum_vulgare";
        }elsif ($temp =~ /Jatropha/) {
                $temp = "Jatropha_curcas";
        }elsif ($temp =~ /Laccaria/) {
@@ -77,8 +85,12 @@ sub find_species {
                $temp = "Neurospora_crassa";
        }elsif ($temp =~ /Nostoc/) {
                $temp = "Nostoc_punctiforme";
+       }elsif ($temp =~ /Oncorhynchus\_mykiss/) {
+               $temp = "Oncorhynchus\_mykiss";
        }elsif ($temp =~ /Oryza\_sativa/) {
                $temp = "Oryza_sativa";
+       }elsif ($temp =~ /Oryzias\_latipes/) {
+               $temp = "Oryzias\_latipes";
        }elsif ($temp =~ /Pediculus/) {
                $temp = "Pediculus_humanus";
        }elsif ($temp =~ /Phoenix/) {
@@ -107,8 +119,16 @@ sub find_species {
                $temp = "Sorghum_bicolor";
        }elsif ($temp =~ /Synechocystis/) {
                $temp = "Synechocystis_pcc6803";
+       }elsif ($temp =~ /Takifugu/) {
+               $temp = "Takifugu\_rubripes";
+       }elsif ($temp =~ /Tetraodon/) {
+               $temp = "Tetraodon\_nigroviridis";
        }elsif ($temp =~ /Theobroma\_cacao/) {
                $temp = "Theobroma_cacao";
+       }elsif ($temp =~ /TmDV92/) {
+               $temp = "TmDV92";
+       }elsif ($temp =~ /TmG3116/) {
+               $temp = "TmG3116";
        }elsif ($temp =~ /Tolypocladium\_inflatum/) {
                $temp = "Tolypocladium_inflatum";
        }elsif ($temp =~ /Trichoderma\_atroviride/) {
@@ -119,6 +139,10 @@ sub find_species {
                $temp = "Trichoderma_virens";
        }elsif ($temp =~ /Trichodesmium/) {
                $temp = "Trichodesmium_erythraeum";
+       }elsif ($temp =~ /triticum\_aestivum/) {
+               $temp = "Triticum_aestivum";
+       }elsif ($temp =~ /Triticum\_urartu/) {
+               $temp = "Triticum_urartu";
        }elsif ($temp =~ /Vitis\_vinifera/) {
                $temp = "Vitis_vinifera";
        }elsif ($temp =~ /Zea\_mays/) {
@@ -134,7 +158,10 @@ sub find_gene {
        $gene_header =~ s/^>//; # strip off the header line identifier, if it isn't already
        my $species = $_[1];
        my $gene;
-       if ($species eq "Arabidopsis_lyrata") {
+       if ($species eq "Aegilops_tauschii") {
+               my ($gene_id, $type, $location, $info) = split(/\s/, $gene_header);
+               $gene = $gene_id;
+       }elsif ($species eq "Arabidopsis_lyrata") {
                my ($name,$gene_id,$scaffold,$isomer) = split(/\|/, $gene_header);
                $gene = $isomer;
        }elsif ($species eq "Arabidopsis_thaliana") {
@@ -191,12 +218,21 @@ sub find_gene {
        }elsif ($species eq "Fusarium_verticilliodes") {
                my ($gene_id, $info) = split(/\s\|\s/, $gene_header);
                $gene = $gene_id;
+       }elsif ($species eq "Gadus_morhua") {
+               my ($gene_id, $transcript_id) = split(/\|/,$gene_header);
+               $gene = $transcript_id;
+       }elsif ($species eq "Gastroerosteus_aculeatus") {
+               my ($gene_id, $transcript_id) = split(/\|/,$gene_header);
+               $gene = $transcript_id;
        }elsif ($species eq "Glycine_max") {
                my ($name,$locus_id,$isomer,$chrom) = split(/\|/,$gene_header);
                $gene = $isomer;
        }elsif ($species eq "Homo_sapiens") {
                my ($protein,$type,$chrom,$gene_id,$transcript) = split(/\s/,$gene_header);
                $gene = $protein;
+       }elsif ($species eq "Hordeum_vulgare") {
+               my ($gene_id,$transcript) = split(/\|/,$gene_header);
+               $gene = $transcript;
        }elsif ($species eq "Jatropha_curcas") {
                my ($gene_id, $temp) = split(/\s/,$gene_header);
                $gene = $gene_id;
@@ -229,9 +265,15 @@ sub find_gene {
        }elsif ($species eq "Nostoc_punctiforme") {
                my ($temp,$transcript,$source,$gene_id,$func) = split(/\|/, $gene_header);
                $gene = $transcript;
+       }elsif ($species eq "Oncorhynchus_mykiss") {
+               my ($gene_id, $offset, $coord_1, $coord_2) = split(/\s/,$gene_header);
+               $gene = $gene_id;
        }elsif ($species eq "Oryza_sativa") {
                my ($isomer,$temp,$type) = split(/\|/,$gene_header);
                $gene = $isomer;
+       }elsif ($species eq "Oryzias_latipes") {
+               my ($gene_id, $transcript_id) = split(/\|/,$gene_header);
+               $gene = $transcript_id;
        }elsif ($species eq "Pediculus_humanus") {
                my ($source,$gene_pa,$func,$unknown,$gene_id) = split(/\|/, $gene_header);
                $gene_id =~ s/gene\://;
@@ -275,9 +317,21 @@ sub find_gene {
        }elsif ($species eq "Synechocystis_pcc6803") {
                my ($gene_id,$temp) = split(" ",$gene_header);
                $gene = $gene_id; #???
+       }elsif ($species eq "Takifugu_rubripes") {
+               my ($gene_id, $transcript_id) = split(/\|/,$gene_header);
+               $gene = $transcript_id;
+       }elsif ($species eq "Tetraodon_nigroviridis") {
+               my ($gene_id, $transcript_id) = split(/\|/,$gene_header);
+               $gene = $transcript_id;
        }elsif ($species eq "Theobroma_cacao") {
                my ($gene_id,$temp) = split(/\s/,$gene_header);
                $gene = $gene_id;
+       }elsif ($species eq "TmDV92") {
+               my ($gene_id,$temp) = split(/\s+/,$gene_header);
+               $gene = $gene_id;
+       }elsif ($species eq "TmG3116") {
+               my ($gene_id,$temp) = split(/\s+/,$gene_header);
+               $gene = $gene_id;       
        }elsif ($species eq "Tolypocladium_inflatum") {
                my ($gene_id, $type, $info) = split(/\s/, $gene_header);
                $gene = $gene_id;
@@ -293,11 +347,18 @@ sub find_gene {
        }elsif ($species eq "Trichodesmium_erythraeum") {
                my ($temp,$unknown,$source,$gene_id,$func) = split(/\|/, $gene_header);
                $gene = $gene_id;
+       }elsif ($species eq "Triticum_aestivum") {
+               my ($type,$transcript,$source,$gene_id,$func) = split(/\|/, $gene_header);
+               $gene = $transcript;
+       }elsif ($species eq "Triticum_urartu") {
+               my ($gene_id, $type, $location, $info) = split(/\s/, $gene_header);
+               $gene = $gene_id;
        }elsif ($species eq "Vitis_vinifera") {
                #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/, $gene_header);
+               #my ($transcript,$seq_type,$coord,$parent_transcript,$parent_gene) = split(/;\s/, $gene_header);
+               my ($spec, $gene_id, $unknown, $transcript) = split(/\|/, $gene_header);
                $gene = $transcript;
                $gene =~ s/\sseq=translation//g;
                
@@ -310,6 +371,7 @@ sub find_gene {
 sub all_species_array {
        # return all species in an array
        my @spec_array;
+       push (@spec_array, "Aegilops_tauschii");
        push (@spec_array, "Arabidopsis_lyrata");
        push (@spec_array, "Arabidopsis_thaliana");
        push (@spec_array, "Batrachochytrium_distachyon");
@@ -330,8 +392,11 @@ sub all_species_array {
        push (@spec_array, "Fusarium_graminearum");
        push (@spec_array, "Fusarium_oxysporum");
        push (@spec_array, "Fusarium_verticilliodes");
+       push (@spec_array, "Gadus_morhua");
+       push (@spec_array, "Gastroerosteus_aculeatus");
        push (@spec_array, "Glycine_max");
        push (@spec_array, "Homo_sapiens");
+       push (@spec_array, "Hordeum_vulgare");
        push (@spec_array, "Jatropha_curcas");
        push (@spec_array, "Laccaria_bicolor");
        push (@spec_array, "Magnaporthe_grissa");
@@ -343,7 +408,9 @@ sub all_species_array {
        push (@spec_array, "Nectria_haematococca");
        push (@spec_array, "Neurospora_crassa");
        push (@spec_array, "Nostoc_punctiforme");
+       push (@spec_array, "Oncorhynchus_mykiss");
        push (@spec_array, "Oryza_sativa");
+       push (@spec_array, "Oryzias_latipes");
        push (@spec_array, "Pediculus_humanus");
        push (@spec_array, "Phoenix_dactylifera");
        push (@spec_array, "Physcomitrella_patens");
@@ -358,12 +425,18 @@ sub all_species_array {
        push (@spec_array, "Solanum_tuberosum");
        push (@spec_array, "Sorghum_bicolor");
        push (@spec_array, "Synechocystis_pcc6803");
+       push (@spec_array, "Takifugu_rubripes");
+       push (@spec_array, "Tetraodon_nigroviridis");
        push (@spec_array, "Theobroma_cacao");
+       push (@spec_array, "TmDV92");
+       push (@spec_array, "TmG3116");
        push (@spec_array, "Tolypocladium_inflatum");
        push (@spec_array, "Trichoderma_atroviride");
        push (@spec_array, "Trichoderma_reesii");
        push (@spec_array, "Trichoderma_virens");
        push (@spec_array, "Trichodesmium_erythraeum");
+       push (@spec_array, "Triticum_aestivum");
+       push (@spec_array, "Triticum_urartu");
        push (@spec_array, "Vitis_vinifera");
        push (@spec_array, "Zea_mays");