--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapsodyn/listfiltering.pl	Fri Oct 10 07:05:36 2014 -0400
@@ -0,0 +1,86 @@
+#!/usr/bin/perl
+# v1.0.1 added log, and two different type of filtering (common / specific)
+use strict;
+use Getopt::Long;
+
+my $list1_file;
+my $list2_file;
+my $log_file;
+my $NB_COL=1;
+my $TYPE = "common";
+my %header;
+my $nb_list1 = 0;
+my $nb_list2 = 0;
+my $nb_common = 0;
+
+
+GetOptions (
+"list1_file=s" => \$list1_file,
+"list2_file=s" => \$list2_file,
+"log_file=s" => \$log_file,
+"type=s" => \$TYPE,
+"nb_col=i" => \$NB_COL
+) or die("Error in command line arguments\n");
+
+open(L2, $list2_file)  or die("Can't open $list2_file\n");
+while (my $line=<L2>){
+	$nb_list2++;
+	chomp($line);
+	my @fields = split(/\s+/,$line);
+	my $ref="";
+	my $compt=0;
+	while ($compt<$NB_COL){
+		if ($ref){$ref.="\t";}
+		$ref.=$fields[$compt];
+		$compt++;
+	}
+	$header{$ref}=$line;
+}
+close (L2);
+
+
+open(L1, $list1_file)  or die("Can't open $list1_file\n");
+while (my $line=<L1>){
+	$nb_list1++;
+	my @fields = split(/\s+/,$line);
+	my $ref="";
+	my $compt=0;
+	while ($compt<$NB_COL){
+		if ($ref){$ref.="\t";}
+		$ref.=$fields[$compt];
+		$compt++;
+	}
+	# my $ref = "$fields[0]\t$fields[1]";
+
+	if ($header{$ref}){
+		$nb_common++;
+		if ($TYPE eq "common"){
+			print $line;
+		}
+		elsif ($TYPE eq "specific") {
+		}
+		else {
+		}
+	}
+	else {
+		if ($TYPE eq "common"){
+		}
+		elsif ($TYPE eq "specific") {
+			print $line;
+		}
+		else {
+		}
+	}
+	
+}
+my $nb_list1_only = $nb_list1 - $nb_common;
+my $nb_list2_only = $nb_list2 - $nb_common;
+
+close(L1);
+open (LF,">$log_file") or die("Can't open $log_file\n");
+print LF "\n####\t List Filtering \n";
+print LF "#List 1 :\t$nb_list1 ($nb_list1_only)\n";
+print LF "#List 2 :\t$nb_list2 ($nb_list2_only)\n";
+print LF "#Common :\t$nb_common\n";
+close (LF);
+