From 598974ae103b3edc99208cdd0c4b22e1a0be086f Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 16 Sep 2009 19:02:46 +0000
Subject: [PATCH] perl script to make batching jobs easier

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1638 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/batchGATKjobsWithRegExp.pl | 57 +++++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100755 perl/batchGATKjobsWithRegExp.pl

diff --git a/perl/batchGATKjobsWithRegExp.pl b/perl/batchGATKjobsWithRegExp.pl
new file mode 100755
index 000000000..d17597d99
--- /dev/null
+++ b/perl/batchGATKjobsWithRegExp.pl
@@ -0,0 +1,57 @@
+#!/usr/bin/perl -w
+
+# Runs a given (GATK) command as specified, except that a single '*'
+# in the -I argument field is replaced with the appropriate shell
+# expansion and all other instances of the '*' in other arguments are
+# replaced with the correct expansion accordingly.
+# IMPORTANT: remember to surround your command with quotes (\"\") so
+# that the shell doesn't try to expand out your regular expression!
+
+use strict;
+use Getopt::Long;
+
+my $dry;
+my $inArg = "I";
+GetOptions( "dry!" => \$dry,
+            "inArg=s" => \$inArg);
+
+if (scalar(@ARGV) != 1) {
+    print "Usage: batchGATKjobsWithRegExp\n\t[-inArg <the GATK argument flag for input; default=I>]\n\t[-dry]\n\t\"GATK command\"\n";
+    exit(1);
+}
+
+my @args = split(/ /, $ARGV[0]);
+chomp(@args);
+
+my $argcount = scalar(@args);
+my $IargIdx = undef;
+for (my $i = 0; $i < $argcount; $i++) {
+    if ($args[$i] eq "-$inArg") {
+	$IargIdx = $i + 1;
+    }
+}
+my $Iarg = "$args[$IargIdx]\n";
+if ($Iarg =~ m/(.*),(.*),(.*)/) {
+    $Iarg = $3;
+}
+my @matches = glob($Iarg);
+$Iarg =~ s/\*/(.*)/;
+chomp($Iarg);
+
+foreach my $match (@matches) {
+    $match =~ m/$Iarg/;
+    my $piece = $1;
+
+    my $cmd = "";
+    for (my $i = 0; $i < $argcount; $i++) {
+	my $arg = $args[$i];
+	$arg =~ s/\*/$piece/;
+	$cmd .= "$arg ";
+    }
+
+    if ($dry) {
+	print "$cmd\n";
+    } else {
+	system($cmd);
+    }
+}