From: elserj <elserj@localhost>
Date: Thu, 16 May 2013 22:30:35 +0000 (+0000)
Subject: Added new fish species
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=f10a0483f2d19ed5012457c04b318d321b85fcfd;p=old-jaiswallab-svn%2F.git

Added new fish species

svn path=/; revision=480
---

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 4f78afd..b532dd9 100755
--- 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");