--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/2.4/script/run_blat.pl	Fri May 30 03:37:55 2014 -0400
@@ -0,0 +1,68 @@
+#####################################################################################################################################################
+#Purpose: To perform blat and organize blat
+#Date: 07-19-2013
+#####################################################################################################################################################
+use Getopt::Long;
+#reading input arguments
+&Getopt::Long::GetOptions(
+'BLAT_PATH=s'=> \$blatpath,
+'REF_FILE=s'=> \$reffile,
+'INPUT_FILE=s' => \$inputfile,
+'OUTPUT_FILE=s' => \$outputfile,
+'MIN_SCORE=s'=> \$minScore,
+'MIN_IDENTITY=s'=> \$minidentity,
+'BLAT_PORT=s'=>\$blatport
+);
+$blatpath =~ s/\s|\t|\r|\n//g;
+$reffile=~ s/\s|\t|\r|\n//g;
+$inputfile=~ s/\s|\t|\r|\n//g;
+$outputfile=~ s/\s|\t|\r|\n//g;
+$minScore=~ s/\s|\t|\r|\n//g;
+$minidentity=~ s/\s|\t|\r|\n//g;
+$blatport=~ s/\s|\t|\r|\n//g;
+#input arguments
+
+#checking for missing arguments
+if($blatport eq "" || $blatpath eq "" || $reffile eq "" || $inputfile eq "" || $outputfile eq "" || $minScore eq "" || $minidentity eq "")
+{
+	die "missing arguments\n USAGE : perl perl_blat.pl -BLAT_PORT <BLAT_PORT> -MIN_SCORE <MIN_SCORE> -MIN_IDENTITY <MIN_IDENTITY> -BLAT_PATH <PATH TO BLAT FOLDER> -REF_FILE <PATH TO 2bit file> -INPUT_FILE <INPUT CONFIG FILE> -OUTPUT_FILE <OUTPUT FILE>\n";
+}
+
+#parsing the arguments
+
+#unless(-d $outdir)
+#{
+#	system("mkdir -p $outdir");
+#}
+$status=`$blatpath/gfServer status localhost $blatport |wc -l`;
+chomp($status);
+$count = 0;
+while($status < 2 )
+{
+	if($count > 0)
+	{
+		$blatport = $blatport+int(rand(1000))+1;
+	}
+	print "Starting the server\n";
+	$sys ="$blatpath/gfServer start -canStop localhost $blatport $reffile &";
+	print "$sys\n";
+	system($sys);
+	sleep(300);
+	$status=`$blatpath/gfServer status localhost $blatport |wc -l`;
+	chomp($status);
+	$count++;
+	if($count > 5)
+	{
+		die "something wrong with gfServer or command . Failed 5 times\n";
+	}
+}	
+print "querying \n";
+$sys = "$blatpath/gfClient localhost $blatport / $inputfile $outputfile -minScore=$minScore -minIdentity=$minidentity";
+print "$sys\n";
+system($sys);
+print "stoping the server\n";
+#$sys = "$blatpath/gfServer stop localhost $blatport";
+$pid = `ps|grep gfServer|head -1|cut -f1 -d ' '`;
+$sys ="kill -9 $pid";
+print "$sys\n";
+system($sys);