From c3416900744e20e864c1d08844f444326a3e8736 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Tue, 16 Dec 2014 23:31:23 +0000
Subject: [PATCH] Updated to work with all species in the 9_9_13 folder. 
 Current as of 12-16-2014

svn path=/; revision=591
---
 interactome_scripts/find_species.pl | 34 +++++++++++++++++++++++++----
 1 file changed, 30 insertions(+), 4 deletions(-)

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 60df470..5e5410e 100755
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -30,6 +30,8 @@ sub find_species {
 		$species = "Brachypodium_sylvaticum.Greece";
 	}elsif ($temp =~ /Brachypodium\_sylvaticum\.Spain/) {
 		$species = "Brachypodium_sylvaticum.Spain";
+	}elsif ($temp =~ /Brassica\_oleracea/) {
+		$species = "Brassica_oleracea";
 	}elsif ($temp =~ /Brassica\_rapa/) {
 		$species = "Brassica_rapa";
 	}elsif ($temp =~ /elegans/) {
@@ -54,6 +56,8 @@ sub find_species {
 		$species = "Citrus_clementina";
 	}elsif ($temp =~ /Citrus\_sinensis/) {
 		$species = "Citrus_sinensis";
+	}elsif ($temp =~ /Coffea\_canephora/) {;
+		$species = "Coffea_canephora";
 	}elsif ($temp =~ /Cucumis\_sativus/) {
 		$species = "Cucumis_sativus";
 	}elsif ($temp =~ /Danio/) {
@@ -184,8 +188,10 @@ sub find_species {
 		$species = "Picea_abies";
 	}elsif ($temp =~ /Pinus/) {
 		$species = "Pinus_taeda";
-	}elsif ($temp =~ /Populus/) {
-		$species = "Populus_trichocarpa";
+	}elsif ($temp =~ /Populus\_trichocarpa\.ver2/) {
+		$species = "Populus_trichocarpa.ver2";
+	}elsif ($temp =~ /Populus\_trichocarpa\.ver3/) {
+		$species = "Populus_trichocarpa.ver3";
 	}elsif ($temp =~ /Prunus/) {
 		$species = "Prunus_persica";
 	}elsif ($temp =~ /Rattus/) {
@@ -270,6 +276,9 @@ sub find_gene {
 	}elsif ($species eq "Brachypodium_sylvaticum.Spain") {
 		my ($gene_id,$temp,$start,$end) = split(/\|/, $gene_header);
 		$gene = $gene_id;
+	}elsif ($species eq "Brassica_oleracea") {
+		my ($protein,$type,$chrom,$gene_id,$transcript) = split(/\s/,$gene_header);
+		$gene = $protein;
 	}elsif ($species eq "Brassica_rapa") {
 		my ($gene_id,$transcript) = split(/\|/, $gene_header);
 		$gene = $transcript; #????
@@ -305,6 +314,9 @@ sub find_gene {
 	}elsif ($species eq "Citrus_sinensis") {
 		my ($transcript_id,$gene_id) = split(/\|/,$gene_header);
 		$gene = $gene_id;
+	}elsif ($species eq "Coffea_canephora") {
+		my ($gene_id, $function) = split(/\s/,$gene_header);
+		$gene = $gene_id;
 	}elsif ($species eq "Cucumis_sativus") {
 		my ($gene_id,$isomer) = split(/\|/,$gene_header);
 		$gene = $isomer;
@@ -509,7 +521,10 @@ sub find_gene {
 	}elsif ($species eq "Pinus_taeda") {
 		my ($gene_id,$type, $AED, $eAED, $qi) = split(/\s/,$gene_header);
 		$gene = $gene_id;
-	}elsif ($species eq "Populus_trichocarpa") {
+	}elsif ($species eq "Populus_trichocarpa.ver2") {
+		my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
+		$gene = $transcript_id;
+	}elsif ($species eq "Populus_trichocarpa.ver3") {
 		my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
 		$gene = $transcript_id;
 	}elsif ($species eq "Prunus_persica") {
@@ -608,6 +623,12 @@ sub find_gene_synonym {
 	if ($species eq "Batrachochytrium_dendrobatidis") {
 		my ($transcript,$gene_id,$info) = split(/\s\|\s/, $gene_header);
 		$synonym = $gene_id;
+	}elsif ($species eq "Brassica_oleracea") {
+		my ($protein,$type,$chrom,$gene_id,$transcript) = split(/\s/,$gene_header);
+		$transcript =~ s/transcript\://;
+		$gene_id =~ s/gene\://;
+		$peptide =~ s/\:pep//;
+		$synonym = "$peptide,$gene_id";
 	}elsif ($species eq "Caenorhabditis_elegans") {
 		my ($locus_id,$unknown,$gene_id,$temp) = split(/\|/, $gene_header);
 		$synonym = $gene_id; #???
@@ -775,7 +796,10 @@ sub find_gene_synonym {
 	}elsif ($species eq "Phytophthora_infestans") {
 		my ($transcript, $gene_id, $function) = split(/\s\|\s/,$gene_header);
 		$synonym = $gene_id;
-	}elsif ($species eq "Populus_trichocarpa") {
+	}elsif ($species eq "Populus_trichocarpa.ver2") {
+		my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
+		$synonym = $gene_id;
+	}elsif ($species eq "Populus_trichocarpa.ver3") {
 		my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
 		$synonym = $gene_id;
 	}elsif ($species eq "Prunus_persica") {
@@ -875,6 +899,7 @@ sub all_species_array {
 	push (@spec_array, "Brachypodium_sylvaticum_Corvallis");
 	push (@spec_array, "Brachypodium_sylvaticum_Greece");
 	push (@spec_array, "Brachypodium_sylvaticum_Spain");
+	push (@spec_array, "Brassica_oleracea");
 	push (@spec_array, "Brassica_rapa");
 	push (@spec_array, "Caenorhabditis_elegans");
 	push (@spec_array, "Cajanus_cajan");
@@ -887,6 +912,7 @@ sub all_species_array {
 	push (@spec_array, "Citrullus_lanatus");
 	push (@spec_array, "Citrus_clementina");
 	push (@spec_array, "Citrus_sinensis");
+	push (@spec_array, "Coffea_canephora");
 	push (@spec_array, "Cucumis_sativus");
 	push (@spec_array, "Danio_rerio");
 	push (@spec_array, "Drosophila_melanogaster");
-- 
2.34.1