From 173c2c03771972b3f605dde5c20105963d9bff5d Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Wed, 6 Jul 2011 23:56:01 +0000
Subject: [PATCH] Added new species

svn path=/; revision=114
---
 interactome_scripts/find_species.pl | 33 +++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 2fdf90e..8b9bb6b 100755
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -4,6 +4,9 @@
 #                                                         #
 #   Written by Justin Elser                               #
 #     Updated 9/2/10 for new species                      #
+#                                                         #
+#     Updated 6/16/11 for new species and added sub       #
+#        to return retrieval info                         #
 ###########################################################
 
 sub find_species {
@@ -52,6 +55,8 @@ sub find_species {
 		$temp = "Glycine_max";
 	}elsif ($temp =~ /Homo\_sapiens/) {
 		$temp = "Homo_sapiens";
+	}elsif ($temp =~ /Jatropha/) {
+		$temp = "Jatropha_curcas";
 	}elsif ($temp =~ /Laccaria/) {
 		$temp = "Laccaria_bicolor";
 	}elsif ($temp =~ /Magnaporthe/) {
@@ -76,6 +81,8 @@ sub find_species {
 		$temp = "Oryza_sativa";
 	}elsif ($temp =~ /Pediculus/) {
 		$temp = "Pediculus_humanus";
+	}elsif ($temp =~ /Phoenix/) {
+		$temp = "Phoenix_dactylifera";
 	}elsif ($temp =~ /Physcomit/) {
 		$temp = "Physcomitrella_patens";
 	}elsif ($temp =~ /Populus/) {
@@ -98,6 +105,8 @@ sub find_species {
 		$temp = "Sorghum_bicolor";
 	}elsif ($temp =~ /Synechocystis/) {
 		$temp = "Synechocystis_pcc6803";
+	}elsif ($temp =~ /Theobroma\_cacao/) {
+		$temp = "Theobroma_cacao";
 	}elsif ($temp =~ /Tolypocladium\_inflatum/) {
 		$temp = "Tolypocladium_inflatum";
 	}elsif ($temp =~ /Trichoderma\_atroviride/) {
@@ -186,6 +195,9 @@ sub find_gene {
 	}elsif ($species eq "Homo_sapiens") {
 		my ($protein,$type,$chrom,$gene_id,$transcript) = split(/\s/,$gene_header);
 		$gene = $protein;
+	}elsif ($species eq "Jatropha_curcas") {
+		my ($gene_id, $temp) = split(/\s/,$gene_header);
+		$gene = $gene_id;
 	}elsif ($species eq "Laccaria_bicolor") {
 		my ($source,$spec,$gene_id,$scaffold) = split(/\|/, $gene_header);
 		$gene = $gene_id;
@@ -222,6 +234,9 @@ sub find_gene {
 		my ($source,$gene_pa,$func,$unknown,$gene_id) = split(/\|/, $gene_header);
 		$gene_id =~ s/gene\://;
 		$gene = $gene_pa;
+	}elsif ($species eq "Phoenix_dactylifera") {
+		my ($gene_id, $temp) = split(/\s/, $gene_header);
+		$gene = $gene_id;
 	}elsif ($species eq "Physcomitrella_patens") {
 		my ($name,$locus_id,$scaffold,$prot_id) = split(/\|/,$gene_header);
 		$gene = $prot_id; #???
@@ -255,6 +270,9 @@ sub find_gene {
 	}elsif ($species eq "Synechocystis_pcc6803") {
 		my ($gene_id,$temp) = split(" ",$gene_header);
 		$gene = $gene_id; #???
+	}elsif ($species eq "Theobroma_cacao") {
+		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 = $gene_id;
@@ -276,6 +294,8 @@ sub find_gene {
 	}elsif ($species eq "Zea_mays") {
 		my ($transcript,$seq_type,$coord,$parent_transcript,$parent_gene) = split(/;\s/, $gene_header);
 		$gene = $transcript;
+		$gene =~ s/\sseq=translation//g;
+		
 	}else {
 		die "Error: Gene id can not be found for species $species!";
 	}
@@ -307,6 +327,7 @@ sub all_species_array {
 	push (@spec_array, "Fusarium_verticilliodes");
 	push (@spec_array, "Glycine_max");
 	push (@spec_array, "Homo_sapiens");
+	push (@spec_array, "Jatropha_curcas");
 	push (@spec_array, "Laccaria_bicolor");
 	push (@spec_array, "Magnaporthe_grissa");
 	push (@spec_array, "Malus_domestica");
@@ -319,6 +340,7 @@ sub all_species_array {
 	push (@spec_array, "Nostoc_punctiforme");
 	push (@spec_array, "Oryza_sativa");
 	push (@spec_array, "Pediculus_humanus");
+	push (@spec_array, "Phoenix_dactylifera");
 	push (@spec_array, "Physcomitrella_patens");
 	push (@spec_array, "Populus_trichocarpa");
 	push (@spec_array, "Prunus_persica");
@@ -330,6 +352,7 @@ sub all_species_array {
 	push (@spec_array, "Selaginella_moellendorffii");
 	push (@spec_array, "Sorghum_bicolor");
 	push (@spec_array, "Synechocystis_pcc6803");
+	push (@spec_array, "Theobroma_cacao");
 	push (@spec_array, "Tolypocladium_inflatum");
 	push (@spec_array, "Trichoderma_atroviride");
 	push (@spec_array, "Trichoderma_reesii");
@@ -340,4 +363,14 @@ sub all_species_array {
 	
 	return @spec_array;
 }
+
+sub retrieval_info {
+	my $file = $_[0];
+	$file =~ /([a-zA-Z]*\_[a-zA-Z0-9]*)\_((?:[a-zA-Z0-9]+\_?)+)\_(\d+\_\d+\_\d+).fa/;
+	my $species = $1;
+	my $method = $2;
+	my $date = $3;
+	return ($method, $date);
+}
+
 1;
-- 
2.34.1