From 0857fc4e2bc729e10f96ab3d9a41d541cacb3729 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Fri, 22 Oct 2010 23:42:26 +0000
Subject: [PATCH] Added new species for Kathryn Bushley

svn path=/; revision=71
---
 interactome_scripts/find_species.pl | 43 +++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 532eeeb..a70083c 100755
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -30,10 +30,18 @@ sub find_species {
 		$temp = "Drosophila_melanogaster";
 	}elsif ($temp =~ /Ectocarpus/) {
 		$temp = "Ectocarpus_siliculosus";
+	}elsif ($temp =~ /Epichloe_festuca/) {
+		$temp = "Epichhloe_festuca";
 	}elsif ($temp =~ /Escherichia\_coli/) {
 		$temp = "Escherichia_coli";
 	}elsif ($temp =~ /Fragaria/) {
 		$temp = "Fragaria_vesca";
+	}elsif ($temp =~ /Fusarium_graminearum/) {
+		$temp = "Fusarium_graminearum";
+	}elsif ($temp =~ /Fusarium_oxysporum/) {
+		$temp = "Fusarium_oxysporum";
+	}elsif ($temp =~ /Fusarium_verticilliodes/) {
+		$temp = "Fusarium_verticilliodes";
 	}elsif ($temp =~ /Glycine/) {
 		$temp = "Glycine_max";
 	}elsif ($temp =~ /Homo\_sapiens/) {
@@ -54,6 +62,8 @@ sub find_species {
 		$temp = "Neurospora_crassa";
 	}elsif ($temp =~ /Nostoc/) {
 		$temp = "Nostoc_punctiforme";
+	}elsif ($temp =~ /Nectria_haematococca/) {
+		$temp = "Nectria_haematococca";
 	}elsif ($temp =~ /Oryza\_sativa/) {
 		$temp = "Oryza_sativa";
 	}elsif ($temp =~ /Pediculus/) {
@@ -80,6 +90,14 @@ sub find_species {
 		$temp = "Sorghum_bicolor";
 	}elsif ($temp =~ /Synechocystis/) {
 		$temp = "Synechocystis_pcc6803";
+	}elsif ($temp =~ /Tolypocladium_inflatum/) {
+		$temp = "Tolypocladium_inflatum";
+	}elsif ($temp =~ /Trichoderma_atroviride/) {
+		$temp = "Trichoderma_atroviride";
+	}elsif ($temp =~ /Trichoderma_reesii/) {
+		$temp = "Trichoderma_reesii";
+	}elsif ($temp =~ /Trichoderma_virens/) {
+		$temp = "Trichoderma_virens";
 	}elsif ($temp =~ /Trichodesmium/) {
 		$temp = "Trichodesmium_erythraeum";
 	}elsif ($temp =~ /Vitis\_vinifera/) {
@@ -130,11 +148,21 @@ sub find_gene {
 	}elsif ($species eq "Ectocarpus_siliculosus") {
 		my ($temp,$transcript,$source,$gene_id,$func) = split(/\|/, $gene_header);
 		$gene = $gene_id;
+	}elsif $species eq "Epichloe_festuca") {
+		$gene = $gene_header;
 	}elsif ($species eq "Escherichia_coli") {
 		$gene = $gene_header; #???
 	}elsif ($species eq "Fragaria_vesca") {
 		my ($gene_id, $mrna_id, $method, $length) = split(/\s\|\s/, $gene_header);
 		$gene = $gene_id;
+	}elsif ($species eq "Fusarium_graminearum") {
+		my ($gene_id, $info) = split(/\s\|\s/, $gene_header);
+		$gene = $gene_id;
+	}elsif ($species eq "Fusarium_oxysporum") {
+		$gene = $gene_header;
+	}elsif ($species eq "Fusarium_verticilliodes") {
+		my ($gene_id, $info) = split(/\s\|\s/, $gene_header);
+		$gene = $gene_id;
 	}elsif ($species eq "Glycine_max") {
 		my ($name,$locus_id,$isomer,$chrom) = split(/\|/,$gene_header);
 		$gene = $isomer;
@@ -162,6 +190,9 @@ sub find_gene {
 	}elsif ($species eq "Neurospora_crassa") {
 		my ($transcript,$gene_id,$temp) = split(/\s\|\s/,$gene_header);
 		$gene = $transcript;
+	}elsif $species eq "Nectria_haematococca") {
+		my ($source, $spec, $int_id, $gene_id) = split(/\|/, $gene_header);
+		$gene = $gene_id;
 	}elsif ($species eq "Nostoc_punctiforme") {
 		my ($temp,$transcript,$source,$gene_id,$func) = split(/\|/, $gene_header);
 		$gene = $gene_id;
@@ -205,9 +236,21 @@ sub find_gene {
 	}elsif ($species eq "Synechocystis_pcc6803") {
 		my ($gene_id,$temp) = split(" ",$gene_header);
 		$gene = $gene_id; #???
+	}elsif ($species eq "Tolypocladium_inflatum") {
+		my ($gene_id, $type, $info) = split(/\s/, $gene_header);
+		$gene = $gene_id;
+	}elsif ($species eq "Trichoderma_atroviride") {
+		my ($source, $spec, $int_id, $gene_id) = split(/\|/,$gene_header);
+		$gene = $gene_id;
+	}elsif ($species eq "Trichoderma_reesii") {
+		my ($source, $spec, $int_id, $gene_id) = split(/\|/,$gene_header);
+		$gene = $gene_id;
 	}elsif ($species eq "Trichodesmium_erythraeum") {
 		my ($temp,$unknown,$source,$gene_id,$func) = split(/\|/, $gene_header);
 		$gene = $gene_id;
+	}elsif ($species eq "Trichoderma_virens") {
+		my ($temp,$unknown,$source,$gene_id,$func) = split(/\|/, $gene_header);
+		$gene = $gene_id;
 	}elsif ($species eq "Vitis_vinifera") {
 		my ($name,$gene_id,$chrom_id,$id) = split(/\|/,$gene_header);
 		$gene = $gene_id; #???
-- 
2.34.1