From: elserj <elserj@localhost>
Date: Fri, 3 Sep 2010 00:24:22 +0000 (+0000)
Subject: Updated the species detection for new species, still need to do gene headers
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=daef375879145f2be4eea958ed22fd74de62346a;p=old-jaiswallab-svn%2F.git

Updated the species detection for new species, still need to do gene headers

svn path=/; revision=24
---

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 1e6c16e..eaf444d 100755
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -2,58 +2,92 @@
 #  Common subroutines to find the species from the        #
 #    string (filename) and the gene from the gene header  #
 #                                                         #
+#   Written by Justin Elser                               #
+#     Updated 9/2/10 for new species                      #
 ###########################################################
 
 sub find_species {
 	my $temp = $_[0];
-	if ($temp =~ /Arabidopsis/) {
-		$temp = "Ath";
-	}elsif ($temp =~ /brachypodium/) {
-		$temp = "Brachy";
+	if ($temp =~ /Arabidopsis\_lyrata/) {
+		$temp = "Arabidopsis_lyrata";
+	}elsif ($temp =~ /Arabidopsis\_thaliana/) {
+		$temp = "Arabidopsis_thaliana";
+	}elsif ($temp =~ /Batrachochytrium/) {
+		$temp = "Batrachochytrium_distachyon";
+	}elsif ($temp =~ /Brachypodium/) {
+		$temp = "Brachypodium_distachyon";
 	}elsif ($temp =~ /elegans/) {
-		$temp = "C_elegans";
+		$temp = "Caenorhabditis_elegans";
+	}elsif ($temp =~ /Carica\_papaya/) {
+		$temp = "Carica_papaya";
 	}elsif ($temp =~ /Chlamy/) {
-		$temp = "Chlamy";
+		$temp = "Chlamydomonas_reinhardtii";
+	}elsif ($temp =~ /Cucumis\_sativus/) {
+		$temp = "Cucumis_sativus";
 	}elsif ($temp =~ /Danio/) {
-		$temp = "Danio";
-	}elsif ($temp =~ /E\_coli/) {
-		$temp = "E_coli";
+		$temp = "Danio_rerio";
+	}elsif ($temp =~ /Drosophila/) {
+		$temp = "Drosophila_melanogaster";
+	}elsif ($temp =~ /Ectocarpus/) {
+		$temp = "Ectocarpus_siliculosus";
+	}elsif ($temp =~ /Escherichia\_coli/) {
+		$temp = "Escherichia_coli";
 	}elsif ($temp =~ /Fragaria/) {
-		$temp = "Fragaria";
+		$temp = "Fragaria_vesca";
 	}elsif ($temp =~ /Glycine/) {
-		$temp = "Glycine";
+		$temp = "Glycine_max";
 	}elsif ($temp =~ /Homo\_sapiens/) {
-		$temp = "Human";
-	}elsif ($temp =~ /Maize/) {
-		$temp = "Maize";
-	}elsif ($temp =~ /musculus/) {
-		$temp = "Mouse";
-	}elsif ($temp =~ /neurospora/) {
-		$temp = "Neurospora";
+		$temp = "Homo_sapiens";
+	}elsif ($temp =~ /Laccaria/) {
+		$temp = "Laccaria_bicolor";
+	}elsif ($temp =~ /Magnaporthe/) {
+		$temp = "Magnaporthe_grissa";
+	}elsif ($temp =~ /Manihot/) {
+		$temp = "Manihot_esculenta";
+	}elsif ($temp =~ /Medicago/) {
+		$temp = "Medicago_truncatula";
+	}elsif ($temp =~ /Mimulus/) {
+		$temp = "Mimulus_guttatus";
+	}elsif ($temp =~ /Mus\_musculus/) {
+		$temp = "Mus_musculus";
+	}elsif ($temp =~ /Neurospora/) {
+		$temp = "Neurospora_crassa";
+	}elsif ($temp =~ /Nostoc/) {
+		$temp = "Nostoc_punctiforme";
 	}elsif ($temp =~ /Oryza\_sativa/) {
 		$temp = "Oryza_sativa";
-	}elsif ($temp =~ /Cpapaya/) {
-		$temp = "Carica_papaya";
+	}elsif ($temp =~ /Pediculus/) {
+		$temp = "Pediculus_humanus";
 	}elsif ($temp =~ /Physcomit/) {
-		$temp = "Physcomitrella";
+		$temp = "Physcomitrella_patens";
 	}elsif ($temp =~ /Populus/) {
-		$temp = "Poplar";
-	}elsif ($temp =~ /Ppersica/) {
-		$temp = "P_persica";
+		$temp = "Populus_trichocarpa";
+	}elsif ($temp =~ /Prunus/) {
+		$temp = "Prunus_persica";
+	}elsif ($temp =~ /Rattus/) {
+		$temp = "Rattus_norvegicus";
+	}elsif ($temp =~ /Rhizopus/) {
+		$temp = "Rhizopus_oryzae";
+	}elsif ($temp =~ /Ricinus/) {
+		$temp = "Ricinus_communis";
 	}elsif ($temp =~ /cerevisiae/) {
-		$temp = "Sacc_cerevisiae";
+		$temp = "Saccharomyces_cerevisiae";
 	}elsif ($temp =~ /pombe/) {
-		$temp = "Schizo_pombe";
+		$temp = "Schizosaccharomyces_pombe";
 	}elsif ($temp =~ /Selaginella/) {
-		$temp = "Selaginella";
+		$temp = "Selaginella_moellendorffii";
 	}elsif ($temp =~ /Sorghum/) {
-		$temp = "Sorghum";
+		$temp = "Sorghum_bicolor";
 	}elsif ($temp =~ /Synechocystis/) {
-		$temp = "Synechocystis";
+		$temp = "Synechocystis_pcc6803";
+	}elsif ($temp =~ /Trichodesmium/) {
+		$temp = "Trichodesmium_erythraeum";
 	}elsif ($temp =~ /Vitis\_vinifera/) {
-		$temp = "Vitis";
+		$temp = "Vitis_vinifera";
+	}elsif ($temp =~ /Zea\_mays/) {
+		$temp = "Zea_mays";
 	}else {
-		die "Error: Species can not be found from file name!";
+		die "Error: Species can not be found from file name $temp!";
 	}
 	return $temp;
 }
@@ -130,7 +164,7 @@ sub find_gene {
 		my ($name,$gene_id,$chrom_id,$id) = split(/\|/,$gene_header);
 		$gene = $gene_id; #???
 	}else {
-		die "Error: Gene id can not be found!";
+		die "Error: Gene id can not be found for species $species!";
 	}
 	return $gene;
 }