Mercurial > repos > vipints > fml_wig2bed

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