From f8e1ea7b64b71c81c5ab2cf86e4311c4a8cceeab Mon Sep 17 00:00:00 2001
From: corin <corin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 15 Nov 2010 19:44:32 +0000
Subject: [PATCH] Script based on the second part of Eric's
 createTranscriptToGenomicInfoTables.pl script which sorts flat files by
 reference order

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4682 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/tablesorter.pl | 49 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 perl/tablesorter.pl

diff --git a/perl/tablesorter.pl b/perl/tablesorter.pl
new file mode 100644
index 000000000..7b8be28d3
--- /dev/null
+++ b/perl/tablesorter.pl
@@ -0,0 +1,49 @@
+#!/usr/bin/perl -w
+
+# sorts by reference
+
+use strict;
+use Getopt::Long;
+
+my $in = undef;
+my $gatk = undef;
+my $ref = undef;
+my $out = undef;
+my $tmp = "/tmp";
+my $contig = undef;
+my $startpos =undef;
+my $mark =undef;
+
+GetOptions( "in=s" => \$in,
+            "gatk=s" => \$gatk,
+            "ref=s" => \$ref,
+            "out=s" => \$out,
+            "tmp=s" => \$tmp,
+            "startpos=s" => \$startpos,
+            "contig=s" => \$contig,
+            "headermarker=s" => \$mark);
+
+	    if ( !$in || !$gatk || !$ref || !$out ) {
+		print "Usage: tablesorter.pl\n\t-in \t\t\t<unsorted input table>\n\t-gatk \t\t\t<path to gatk trunk>\n\t-ref \t\t\t<path to reference.fasta>\n\t-out \t\t\t<sorted output table>\n\t-tmp \t\t\t<temp file location; needs potentially lots of space; defaults to /tmp>\n\t-startpos \t\t<Which column is your start position listed in?>\n\t-contig \t\t<Which column is your contig listed in?>\n\t-headermarker \t\t<Give a field name unique to your header (not found in your table).>\n";
+		print "Example: ./tablesorter.pl\n\t-in test.foo\n\t-ref /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta\n\t-gatk /humgen/gsa-s r1/ebanks/Sting_dev\n\t-out test.bar\n\t-tmp /broad/shptmp\n\t-startpos /2\n\t-contig 1\n\t-headermarker haplotype \n";
+		exit(1);
+	    }
+
+
+# we need to sort the converted table now
+	    print "\nSorting the table...\n";
+	    open(SORTED, ">$out") or die "can't open $out: $!";
+
+# write the header
+	    open(UNSORTED, "< $in") or die "can't open $in: $!";
+	    my $line = <UNSORTED>;
+	    print SORTED "$line";
+	    close(UNSORTED);
+	    close(SORTED);
+
+print "$line is the header";
+	    my $cmd = "grep $mark -v $in | sort -n -k$startpos -T $tmp | $gatk/perl/sortByRef.pl --k $contig --tmp $tmp - $ref.fai >> $out";
+	    system($cmd);
+# clean upunlink $unsorted_table;
+
+	    print "\nDone!\n";