Mercurial > repos > vipints > fml_wig2bed

comparison Wig_to_bedGraph/script/wig2bedGraph_converter.pl @ 0:45f3fa82369f default tip

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author vipints
date Tue, 07 Jun 2011 18:08:31 -0400
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-1:000000000000 0:45f3fa82369f
1 #!/usr/bin/env perl
2 #
3 # This program is free software; you can redistribute it and/or modify
4 # it under the terms of the GNU General Public License as published by
5 # the Free Software Foundation; either version 3 of the License, or
6 # (at your option) any later version.
7 #
8 # Written (W) 2010 Vipin T. Sreedharan, Friedrich Miescher Laboratory of the Max Planck Society
9 # Copyright (C) 2010 Max Planck Society
10 #
11 # Description: - read fixedStep and variableStep wiggle input data,
12 # output four column bedGraph format data
13
14 use warnings;
15 use strict;
16
17 my ($position, $chr, $step, $span) = (0, "", 1, 1);
18
19 my $usage = q(
20 fixedStep2BED.pl - Program to convert a valid fixedStep or variableStep wiggle input data to BED format.
21 USAGE: wig2bedGraph_converter <fixedStep/variableStep Wiggle format> > <output file name>
22
23 );
24 if (scalar(@ARGV) != 1) {
25 print $usage;
26 exit
27 }
28
29 my $inFile = $ARGV[0];
30 open WIG, "<$inFile" || die "Can't open the Wiggle file \n";
31 while (my $dataValue = <WIG>)
32 {
33 chomp $dataValue;
34 next if ( $dataValue =~ m/^track /);
35 if ( $dataValue =~ m/^fixedStep/ || $dataValue =~ m/^variableStep/ ) {
36 ($position, $chr, $step, $span) = (0, "", 1, 1);
37 my @a = split('\s', $dataValue);
38 for (my $i = 1; $i < scalar(@a); ++$i) {
39 my ($ident, $value) = split('=',$a[$i]);
40 if ($ident =~ m/chrom/) { $chr = $value; }
41 elsif ($ident =~ m/start/) { $position = $value-1; }
42 elsif ($ident =~ m/step/) { $step = $value; }
43 elsif ($ident =~ m/span/) { $span = $value; }
44 else {
45 print STDERR "ERROR: unrecognized fixedStep/variableStep line: $dataValue\n";
46 exit 255;
47 }
48 }
49 }
50 else {
51 my @b = split('\s', $dataValue);
52 if (scalar(@b)>1) {
53 $position = $b[0];
54 $dataValue = $b[1];
55 }
56 my $loc_pos = $position+$span;
57 print "$chr\t$position\t$loc_pos\t$dataValue\n";
58 $position = $position + $step;
59 }
60 }
61 close WIG;
62 exit;