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comparison windowmasker_to_bed.pl @ 0:d90ae4a02efd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ commit d529dafd5a2d3a017de226cd59e42cf630348e06
author iuc
date Thu, 14 Dec 2023 16:04:27 +0000
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-1:000000000000 0:d90ae4a02efd
1 #!/usr/bin/env perl
2 use warnings;
3 use strict;
4
5 =head1 NAME
6
7 windowmasker_to_bed.pl - Convert WindowMasker output to BED format
8
9 =head1 SYNOPSIS
10
11 windowmasker_to_bed.pl < ${input.interval} > ${output.bed}
12
13 =head1 DESCRIPTION
14
15 This scripts converts the interval output from WindowMasker ustat
16 to bed 4 format.
17
18 =head1 VERSION
19
20 Last update: 2017-04-28
21
22 =cut
23
24
25 #====================
26 # Libraries
27 #====================
28 use Getopt::Long;
29 use Pod::Usage;
30 use Carp;
31
32 sub main {
33 parse_arguments();
34
35 my $chrom;
36 my $idx = 0;
37
38 while ( defined(my $line = <>) ) {
39 next if ($line =~ /^\s*$/x);
40
41 if ($line =~ /^>(\S+)/x) {
42 $chrom = $1;
43
44 } elsif ($line =~ /(\d+)\s+\-\s+(\d+)/x) {
45 # interval coordinates are 0-based
46 my $start = $1;
47 my $end = $2 + 1;
48 my $name = sprintf("wm_%d", $idx++);
49
50 print join("\t", $chrom, $start, $end, $name), "\n";
51
52 } else {
53 croak("Invalid line: ${line}");
54 }
55 }
56
57 return;
58 }
59
60 main();
61
62
63
64 #====================
65 # Parse command-line arguments
66 #====================
67 sub parse_arguments {
68 my $help = 0;
69
70 GetOptions('help|?' => \$help) or usage();
71
72 pod2usage({ verbose => 2 }) if ($help);
73
74 return;
75 }
76
77 sub usage {
78 my $msg = shift;
79
80 pod2usage({ verbose => 1, message => $msg || "" });
81 exit 1;
82 }