From: elserj <elserj@localhost>
Date: Tue, 7 Sep 2010 22:22:07 +0000 (+0000)
Subject: Added script to find interactions given a list of genes
X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=968a02f1c8d4430366d9c7c666d8c0d207202ff6;p=old-jaiswallab-svn%2F.git

Added script to find interactions given a list of genes

svn path=/; revision=30
---

diff --git a/interactome_scripts/find_matching_interactions.pl b/interactome_scripts/find_matching_interactions.pl
new file mode 100755
index 0000000..1fc77cf
--- /dev/null
+++ b/interactome_scripts/find_matching_interactions.pl
@@ -0,0 +1,40 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+# program to take a list of genes, and find all interactions in an interaction file (sif format) 
+#     where both interaction genes are in the list
+
+if($#ARGV != 2) {
+	print "usage: find_matching_interactions.pl input_gene_list interaction_file output_file\n";
+	exit;
+}
+
+my $in_file = $ARGV[0];
+my $inter_file = $ARGV[1];
+my $out_file = $ARGV[2];
+
+# read in the genes to look for
+open (in_file, "$in_file");
+
+my %in_hash;
+while(<in_file>) {
+	my $line = $_;
+	chomp $line;
+	
+	$in_hash{$line} = $line;
+}
+
+# read in the interaction file and do the lookups
+open (inter_file, "$inter_file");
+open (out_file, ">$out_file");
+
+while(<inter_file>) {
+	my $line = $_;
+	chomp $line;
+	my ($inter_1, $type, $inter_2) = split("\t", $line);
+	if(defined($in_hash{$inter_1}) && defined($in_hash{$inter_2}) ) {
+		print out_file "$line\n";
+	}
+}