From 6b14d46c6fd519635b2a56f96eb2659a2a65384a Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Wed, 2 Jun 2010 20:39:48 +0000
Subject: [PATCH] Updated scripts

svn path=/; revision=17
---
 interactome_scripts/find_ortho_super.pl | 21 ++++++++++++++++++---
 interactome_scripts/find_species.pl     | 16 +++++++++-------
 2 files changed, 27 insertions(+), 10 deletions(-)

diff --git a/interactome_scripts/find_ortho_super.pl b/interactome_scripts/find_ortho_super.pl
index 45cbfa9..ca7af46 100755
--- a/interactome_scripts/find_ortho_super.pl
+++ b/interactome_scripts/find_ortho_super.pl
@@ -52,6 +52,10 @@ for (my $i = 1; $i<$spec_array_size; $i++) {
 	
 	# set up db query statement to get the orthologs using the cluster id
 	my $sth_get_ortho = $dbh->prepare("select gene from $table where super_id = ? and species = '$species_array[$i]'");
+	#my $sth_get_ortho = $dbh->prepare("select gene,species from $table where super_id = ?");
+	
+	# setup query to make sure there is an ortholog gene in the cluster
+	my $sth_check_ortho = $dbh->prepare("select species from $table where super_id = ? and species = '$species_array[0]'");
 	
 	foreach my $gene (@in_gene_array) {
 		
@@ -61,12 +65,23 @@ for (my $i = 1; $i<$spec_array_size; $i++) {
 		}
 		
 		while (my $id = $sth_get_id->fetchrow_array()) {
-			my $rv2 = $sth_get_ortho->execute($id);
-			if (!$rv2) {
+			#my $rv2 = $sth_check_ortho->execute($id);
+			#if (!$rv2) {
+			#	next;
+			#}
+			#my $check = $sth_check_ortho->fetchrow_array();
+			#print "$id\t$check\n";
+			#if ($check ne "$species_array[0]") {
+			#	print "no match\t\t$id\t$check\n";
+			#	next;
+			#}
+			
+			my $rv3 = $sth_get_ortho->execute($id);
+			if (!$rv3) {
 				next;
 			}
 			
-			while (my $ortho = $sth_get_ortho->fetchrow_array()) {
+			while (my ($ortho, $species) = $sth_get_ortho->fetchrow_array()) {
 				print out_file "$gene\t$ortho\n";
 			}
 		}
diff --git a/interactome_scripts/find_species.pl b/interactome_scripts/find_species.pl
index 17c7a88..1e6c16e 100755
--- a/interactome_scripts/find_species.pl
+++ b/interactome_scripts/find_species.pl
@@ -32,8 +32,10 @@ sub find_species {
 		$temp = "Neurospora";
 	}elsif ($temp =~ /Oryza\_sativa/) {
 		$temp = "Oryza_sativa";
+	}elsif ($temp =~ /Cpapaya/) {
+		$temp = "Carica_papaya";
 	}elsif ($temp =~ /Physcomit/) {
-		$temp = "Physcomitreall";
+		$temp = "Physcomitrella";
 	}elsif ($temp =~ /Populus/) {
 		$temp = "Poplar";
 	}elsif ($temp =~ /Ppersica/) {
@@ -41,13 +43,13 @@ sub find_species {
 	}elsif ($temp =~ /cerevisiae/) {
 		$temp = "Sacc_cerevisiae";
 	}elsif ($temp =~ /pombe/) {
-		$temp = "Sacc_pombe";
+		$temp = "Schizo_pombe";
 	}elsif ($temp =~ /Selaginella/) {
 		$temp = "Selaginella";
 	}elsif ($temp =~ /Sorghum/) {
 		$temp = "Sorghum";
-	}elsif ($temp =~ /Synechosystis/) {
-		$temp = "Synechosystis";
+	}elsif ($temp =~ /Synechocystis/) {
+		$temp = "Synechocystis";
 	}elsif ($temp =~ /Vitis\_vinifera/) {
 		$temp = "Vitis";
 	}else {
@@ -100,7 +102,7 @@ sub find_gene {
 	}elsif ($species eq "Oryza_sativa") {
 		my ($isomer,$temp,$type) = split(/\|/,$gene_header);
 		$gene = $isomer;
-	}elsif ($species eq "Physcomitreall") {
+	}elsif ($species eq "Physcomitrella") {
 		my ($name,$locus_id,$chrom_id,$prot_id) = split(/\|/,$gene_header);
 		$gene = $prot_id; #???
 	}elsif ($species eq "Poplar") {
@@ -112,7 +114,7 @@ sub find_gene {
 	}elsif ($species eq "Sacc_cerevisiae") {
 		my ($gene_id,$temp) = split(/\s/,$gene_header);
 		$gene = $gene_id;
-	}elsif ($species eq "Sacc_pombe") {
+	}elsif ($species eq "Schizo_pombe") {
 		my ($gene_id,$temp) = split(/\s/,$gene_header);
 		$gene = $gene_id;
 	}elsif ($species eq "Selaginella") {
@@ -121,7 +123,7 @@ sub find_gene {
 	}elsif ($species eq "Sorghum") {
 		my ($name,$locus_id,$scaff_id,$prot_id) = split(/\|/,$gene_header);
 		$gene = $prot_id; #???
-	}elsif ($species eq "Synechosystis") {
+	}elsif ($species eq "Synechocystis") {
 		my ($gene_id,$type,$temp) = split(" ",$gene_header);
 		$gene = $gene_id; #???
 	}elsif ($species eq "Vitis") {
-- 
2.34.1