From 36058bce23f8c3bbd84f4dddd424c23943b51f88 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Wed, 14 Apr 2010 21:19:14 +0000
Subject: [PATCH] Split find_ortho scripts to do it from the super_clust table
 instead of inparanoid

svn path=/; revision=16
---
 interactome_scripts/find_ortho_inpara.pl | 11 ++--
 interactome_scripts/find_ortho_super.pl  | 76 ++++++++++++++++++++++++
 2 files changed, 83 insertions(+), 4 deletions(-)
 create mode 100755 interactome_scripts/find_ortho_super.pl

diff --git a/interactome_scripts/find_ortho_inpara.pl b/interactome_scripts/find_ortho_inpara.pl
index 51d9504..08fca80 100755
--- a/interactome_scripts/find_ortho_inpara.pl
+++ b/interactome_scripts/find_ortho_inpara.pl
@@ -32,13 +32,15 @@ my @in_gene_array;
 while(<in_file>) {
 	my $in_gene = $_;
 	chomp $in_gene;	
+	$in_gene =~ s/\s//g;
 	$in_gene .= ".1"; # add the suffix back so that the gene matches the db
 	push(@in_gene_array, $in_gene);
+	#print "$in_gene\n";
 	
 }
 close(in_file);
 
-open(out_file, ">flower_ortho.txt");
+open(out_file, ">Ath_ortho.txt");
 
 for (my $i = 1; $i<$spec_array_size; $i++) {
 	
@@ -49,7 +51,7 @@ for (my $i = 1; $i<$spec_array_size; $i++) {
 	my $sth_get_id = $dbh->prepare("select id from $table where gene = ?");
 	
 	# set up db query statement to get the orthologs using the cluster id
-	my $sth_get_ortho = $dbh->prepare("select gene from $table where id = ? and species = '$species_array[$i]' and score = '1'");
+	my $sth_get_ortho = $dbh->prepare("select gene, score from $table where id = ? and species = '$species_array[$i]' and score >= '0.0'");
 	
 	foreach my $gene (@in_gene_array) {
 		
@@ -64,8 +66,9 @@ for (my $i = 1; $i<$spec_array_size; $i++) {
 				next;
 			}
 			
-			while (my $ortho = $sth_get_ortho->fetchrow_array()) {
-				print out_file "$gene\t$ortho\n";
+			while (my @line = $sth_get_ortho->fetchrow_array()) {
+				my ($ortho,$score) = @line;
+				print out_file "$gene\t$ortho\t$score\n";
 			}
 		}
 	}
diff --git a/interactome_scripts/find_ortho_super.pl b/interactome_scripts/find_ortho_super.pl
new file mode 100755
index 0000000..45cbfa9
--- /dev/null
+++ b/interactome_scripts/find_ortho_super.pl
@@ -0,0 +1,76 @@
+#!/usr/bin/perl
+
+#####################################################################
+#    Written by Justin Elser 4/14/10                                #
+#                                                                   #
+#    This program takes an input file with a list of genes and      #
+#      finds the orthologs (and paralogs if the score in sth_get_ortho #
+#      is changed).                                                 #
+#                                                                   #
+#####################################################################
+
+use strict;
+use warnings;
+
+use lib "$ENV{HOME}/scripts/jaiswallab/interactome_scripts";
+
+use DbiFloret;
+
+my $dbh = DbiFloret::dbconnect;
+
+#my @species_array = ("Ath", "Oryza_sativa", "Sorghum", "Maize", "Glycine");
+my @species_array = ("Ath", "Maize");
+my $spec_array_size = @species_array;
+
+# read in list of genes from csv file given as argument
+my $in_file = $ARGV[0];
+
+open (in_file, "$in_file");
+
+my @in_gene_array;
+
+while(<in_file>) {
+	my $in_gene = $_;
+	chomp $in_gene;	
+	$in_gene =~ s/\s//g;
+	$in_gene .= ".1"; # add the suffix back so that the gene matches the db
+	push(@in_gene_array, $in_gene);
+	#print "$in_gene\n";
+	
+}
+close(in_file);
+
+open(out_file, ">Ath_ortho_super.txt");
+
+for (my $i = 1; $i<$spec_array_size; $i++) {
+	
+	my $table = "super_clust";
+	#print out_file "$species_array[$i]\t$table\n";
+	
+	# set up the db query statement
+	my $sth_get_id = $dbh->prepare("select super_id from $table where gene = ?");
+	
+	# 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]'");
+	
+	foreach my $gene (@in_gene_array) {
+		
+		my $rv1 = $sth_get_id->execute($gene);
+		if (!$rv1) {
+			next;
+		}
+		
+		while (my $id = $sth_get_id->fetchrow_array()) {
+			my $rv2 = $sth_get_ortho->execute($id);
+			if (!$rv2) {
+				next;
+			}
+			
+			while (my $ortho = $sth_get_ortho->fetchrow_array()) {
+				print out_file "$gene\t$ortho\n";
+			}
+		}
+	}
+}
+
+close(out_file);
-- 
2.34.1