From ecfbc2c13cf5a66b0a201ccdcc29bc92b52929a2 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Fri, 14 Mar 2014 00:43:09 +0000
Subject: [PATCH] Fixed Zea and added new species

svn path=/; revision=537
---
 interactome_scripts/find_species.pl | 45 ++++++++++++++++++++++++-----
 1 file changed, 37 insertions(+), 8 deletions(-)

diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 196712f..78079c2 100755
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -36,12 +36,18 @@ sub find_species {
 		$species = "Caenorhabditis_elegans";
 	}elsif ($temp =~ /Cajanus\_cajan/) {
 		$species = "Cajanus_cajan";
+	}elsif ($temp =~ /Cannabis/) {
+		$species = "Cannabis_sativa.Purple.Kush";
+	}elsif ($temp =~ /Capsella/) {
+		$species = "Capsella_rubella";
 	}elsif ($temp =~ /Carica\_papaya/) {
 		$species = "Carica_papaya";
 	}elsif ($temp =~ /Chlamy/) {
 		$species = "Chlamydomonas_reinhardtii";
 	}elsif ($temp =~ /Cicer\_arietinum/) {
 		$species = "Cicer_arietinum";
+	}elsif ($temp =~ /Citrullus\_lanatus/) {
+		$species = "Citrullus_lanatus";
 	}elsif ($temp =~ /Citrus\_clementina/) {
 		$species = "Citrus_clementina";
 	}elsif ($temp =~ /Citrus\_sinensis/) {
@@ -110,6 +116,8 @@ sub find_species {
 		$species = "Musa_acuminata";
 	}elsif ($temp =~ /Nectria\_haematococca/) {
 		$species = "Nectria_haematococca";
+	}elsif ($temp =~ /Nelumbo/) {
+		$species = "Nelumbo_nucifera";
 	}elsif ($temp =~ /Neurospora/) {
 		$species = "Neurospora_crassa";
 	}elsif ($temp =~ /Nostoc/) {
@@ -261,6 +269,12 @@ sub find_gene {
 	}elsif ($species eq "Cajanus_cajan") {
 		my ($gene_id,$type,$locus,$temp) = split(/\s/, $gene_header);
 		$gene = $gene_id;
+	}elsif ($species eq "Cannabis_sativa.Purple.Kush") {
+		my ($gene_id, $strand, $start, $stop) = split(/\t/, $gene_header);
+		$gene = $gene_id;
+	}elsif ($species eq "Capsella_rubella") {
+		my ($gene_id, $transcript) = split(/\|/, $gene_header);
+		$gene = $transcript;
 	}elsif ($species eq "Carica_papaya") {
 		my ($contig,$gene_id) = split(/\|/, $gene_header);
 		$gene = $gene_id;
@@ -270,6 +284,9 @@ sub find_gene {
 	}elsif ($species eq "Cicer_arietinum") {
 		my ($gi,$number,$ref,$gene_id,$function) = split(/\|/, $gene_header);
 		$gene = $gene_id;
+	}elsif ($species eq "Citrullus_lanatus") {
+		my ($gene_id, $type, $locus, $method) = split(/\s/, $gene_header);
+		$gene = $gene_id;
 	}elsif ($species eq "Citrus_clementina") {
 		my ($transcript_id,$gene_id) = split(/\|/,$gene_header);
 		$gene = $gene_id;
@@ -376,6 +393,9 @@ sub find_gene {
 		my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
 		$transcript =~ s/transcript\://;
 		$gene = $transcript;
+	}elsif ($species eq "Nelumbo_nucifera") {
+		my ($gene_id, $temp) = split(/\s/, $gene_header);
+		$gene = $gene_id;
 	}elsif ($species eq "Neurospora_crassa") {
 		my ($transcript,$gene_id,$temp) = split(/\s\|\s/,$gene_header);
 		$gene = $transcript;
@@ -467,10 +487,8 @@ sub find_gene {
 		my ($gene_id, $confidence) = split(/\s/,$gene_header);
 		$gene = $gene_id;
 	}elsif ($species eq "Pinus_taeda") {
-		my ($gene_id,$temp) = split(/\:/,$gene_header);
-		$gene_id =~ /\D+(\d+)/;
-		print "$1\n";
-		$gene = $1;
+		my ($gene_id,$type, $AED, $eAED, $qi) = split(/\s/,$gene_header);
+		$gene = $gene_id;
 	}elsif ($species eq "Populus_trichocarpa") {
 		my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
 		$gene = $transcript_id;
@@ -548,8 +566,9 @@ sub find_gene {
 		my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
 		$gene = $gene_id;
 	}elsif ($species eq "Zea_mays") {
-		my ($gene_id,$transcript) = split(/\|/,$gene_header);
-		$gene = $transcript;
+		my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
+        $transcript =~ s/transcript\://;
+        $gene = $transcript;
 		
 	}else {
 		die "Error: Gene id can not be found for species $species!";
@@ -572,6 +591,9 @@ sub find_gene_synonym {
 	}elsif ($species eq "Cajanus_cajan") {
 		my ($gene_id,$type,$locus,$temp) = split(/\s/, $gene_header);
 		$synonym = $locus;
+	}elsif ($species eq "Capsella_rubella") {
+		my ($gene_id, $transcript) = split(/\|/, $gene_header);
+		$synonym = $gene_id;
 	}elsif ($species eq "Carica_papaya") {
 		my ($contig,$gene_id) = split(/\|/, $gene_header);
 		$synonym = $contig;
@@ -805,8 +827,11 @@ sub find_gene_synonym {
 		my ($gene_id,$transcript_id) = split(/\|/,$gene_header);
 		$synonym = $transcript_id;
 	}elsif ($species eq "Zea_mays") {
-		my ($gene_id,$transcript) = split(/\|/,$gene_header);
-		$synonym = $gene_id;
+		my ($peptide,$temp,$chrom,$gene_id,$transcript,$gene_type,$transcript_type) = split(/\s/,$gene_header);
+        $transcript =~ s/transcript\://;
+        $gene_id =~ s/gene\://;
+        $peptide =~ s/\:pep//;
+        $synonym = "$peptide,$gene_id";
 		
 	}else {
 		$synonym = "null";
@@ -830,9 +855,12 @@ sub all_species_array {
 	push (@spec_array, "Brassica_rapa");
 	push (@spec_array, "Caenorhabditis_elegans");
 	push (@spec_array, "Cajanus_cajan");
+	push (@spec_array, "Cannabis_sativa.Purple.Kush");
+	push (@spec_array, "Capsella_rubella");
 	push (@spec_array, "Carica_papaya");
 	push (@spec_array, "Chlamydomonas_reinhardtii");
 	push (@spec_array, "Cicer_arietinum");
+	push (@spec_array, "Citrullus_lanatus");
 	push (@spec_array, "Citrus_clementina");
 	push (@spec_array, "Citrus_sinensis");
 	push (@spec_array, "Cucumis_sativus");
@@ -866,6 +894,7 @@ sub all_species_array {
 	push (@spec_array, "Mus_musculus");
 	push (@spec_array, "Musa_acuminata");
 	push (@spec_array, "Nectria_haematococca");
+	push (@spec_array, "Nelumbo_nucifera");
 	push (@spec_array, "Neurospora_crassa");
 	push (@spec_array, "Nostoc_punctiforme");
 	push (@spec_array, "Oncorhynchus_mykiss");
-- 
2.34.1