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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
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corin 2010-11-15 19:44:32 +00:00
parent 2af508ef83
commit f8e1ea7b64
1 changed files with 49 additions and 0 deletions
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perl/tablesorter.pl 100644
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#!/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";