Mercurial > repos > yating-l > windowmasker_2_5_0

annotate windowmasker_to_bed.pl @ 0:f80c9e6700ba draft default tip

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planemo upload commit 91a780909d1eda07d17f6aebf7f08f0c024b6a25
author yating-l
date Tue, 16 May 2017 13:18:12 -0400
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1 #!/usr/bin/env perl
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2 use warnings;
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3 use strict;
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4
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5 =head1 NAME
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6
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7 windowmasker_to_bed.pl - Convert WindowMasker output to BED format
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8
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9 =head1 SYNOPSIS
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10
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11 windowmasker_to_bed.pl < ${input.interval} > ${output.bed}
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12
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13 =head1 DESCRIPTION
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14
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15 This scripts converts the interval output from WindowMasker ustat
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16 to bed 4 format.
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17
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18 =head1 VERSION
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19
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20 Last update: 2017-04-28
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21
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22 =cut
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23
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24
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25 #====================
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26 # Libraries
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27 #====================
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28 use Getopt::Long;
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29 use Pod::Usage;
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30 use Carp;
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31
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32 sub main {
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33 parse_arguments();
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34
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35 my $chrom;
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36 my $idx = 0;
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37
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38 while ( defined(my $line = <>) ) {
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39 next if ($line =~ /^\s*$/x);
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40
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41 if ($line =~ /^>(\S+)/x) {
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42 $chrom = $1;
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43
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44 } elsif ($line =~ /(\d+)\s+\-\s+(\d+)/x) {
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45 # interval coordinates are 0-based
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46 my $start = $1;
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47 my $end = $2 + 1;
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48 my $name = sprintf("wm_%d", $idx++);
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49
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50 print join("\t", $chrom, $start, $end, $name), "\n";
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51
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52 } else {
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53 croak("Invalid line: ${line}");
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54 }
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55 }
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56
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57 return;
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58 }
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59
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60 main();
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61
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62
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63
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64 #====================
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65 # Parse command-line arguments
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66 #====================
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67 sub parse_arguments {
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68 my $help = 0;
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69
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70 GetOptions('help|?' => \$help) or usage();
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71
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72 pod2usage({ verbose => 2 }) if ($help);
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73
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74 return;
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75 }
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76
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77 sub usage {
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78 my $msg = shift;
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79
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80 pod2usage({ verbose => 1, message => $msg || "" });
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81 exit 1;
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82 }