Mercurial > repos > jdv > nanopolish

annotate nanopolish_variants.pl @ 6:36cc4ae4160e draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit d47b131af7d3a9f8446732f91ec08503c99aab58
author jdv
date Mon, 04 Dec 2017 02:03:21 -0500
parents bdd6c1ab07c5
children 32cb27adeb34
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2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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1 #!/usr/bin/env perl
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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2
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3 use strict;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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4 use warnings;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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5 use 5.012;
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6
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7 use Cwd qw/getcwd abs_path/;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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8 use File::Copy qw/copy/;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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9 use Getopt::Long qw/:config pass_through/;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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10 use threads;
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11 use threads::shared;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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12 use BioX::Seq::Stream;
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13
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14 my $fn_genome;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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15 my $threads = 1;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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16 my $fn_outfile;
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17 my $fn_consensus;
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18 my $fn_fast5;
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19 my $fn_reads;
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21 # remember full command string (with proper binary)
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23 # parse genome filename and add back to arg stack
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24 GetOptions(
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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25 'genome=s' => \$fn_genome,
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26 'threads=i' => \$threads,
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27 'outfile=s' => \$fn_outfile,
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28 'consensus=s' => \$fn_consensus,
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29 'fast5=s' => \$fn_fast5,
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30 'reads=s' => \$fn_reads,
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31 );
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33 my $ret;
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34
0
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35 my $tmp_dir = 'tmp_dir';
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36 mkdir $tmp_dir;
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37
3
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38 $fn_fast5 = abs_path($fn_fast5);
a1d433401bc2 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit e9238df905c413aaab086ea146cb1b97e3ffa0fd
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39
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40 # extract FAST5 files to path where they are expected
4
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41 # use system 'tar' to transparently and safely handle absolute paths
3
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42 my $fast5_dir = 'fast5';
a1d433401bc2 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit e9238df905c413aaab086ea146cb1b97e3ffa0fd
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43 mkdir $fast5_dir;
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44 my $cwd = abs_path( getcwd() );
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45 chdir $fast5_dir;
4
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46 $ret = system(
bdd6c1ab07c5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 83364d7d78ca5524a08065daef995bfcd54a379d
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47 'tar',
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48 '-xvf',
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49 $fn_fast5
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50 );
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51 die "Failed to extract tarball: $!\n"
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52 if ($ret);
0
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53 chdir $cwd;
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54
3
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55
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56 # index reads
4
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57 $ret = system(
3
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58 'nanopolish',
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59 'index',
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60 '--directory' => $fast5_dir,
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61 $fn_reads,
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62 );
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63 die "Failed nanopolish indexing: $!\n"
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64 if ($ret);
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65
0
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66 my @cmd = @ARGV;
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67 unshift @cmd, 'nanopolish';
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68 push @cmd, '--genome', $fn_genome;
3
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69 push @cmd, '--reads', $fn_reads;
0
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70
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71 my @regions :shared;
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72
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73 # build region tags to pass to nanopolish
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74 my $parser = BioX::Seq::Stream->new($fn_genome);
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75 while (my $seq = $parser->next_seq) {
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76 push @regions, join( ':', $seq->id,
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77 join( '-', 1, length($seq) ),
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78 );
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79 }
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80
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81 my @workers;
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82 for (1..$threads) {
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83 push @workers, threads->create(\&run);
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84 }
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85
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86 $_->join() for (@workers);
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87
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88 my @fa_files = glob "$tmp_dir/*.fasta";
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89 my @out_files = glob "$tmp_dir/*.vcf";
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90
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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91 open my $out_cons, '>', $fn_consensus
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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92 or die "Failed to open output consensus: $!";
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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93 for (@fa_files) {
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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94 open my $in, '<', $_;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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95 while (my $line = <$in>) {
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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96 print {$out_cons} $line;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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97 }
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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98 close $in;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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99 }
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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100 close $out_cons;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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101
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102 # we may need to do extra processing on VCF output
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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103 open my $out_vcf, '>', $fn_outfile
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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104 or die "Failed to open output file: $!";
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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105 for my $i (0..$#out_files) {
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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106 my $v = $out_files[$i];
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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107 open my $in, '<', $v;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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108 while (my $line = <$in>) {
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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109 next if ($line =~ /^\s*#/ && $i > 0);
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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110 print {$out_vcf} $line;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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111 }
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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112 close $in;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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113 }
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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114 close $out_vcf;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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115
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116
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117 sub run {
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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118
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119 LOOP:
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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120 while (1) {
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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121
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122 my $tag;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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123
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124 {
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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125 lock @regions;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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126 last LOOP if (! scalar @regions);
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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127 $tag = shift @regions;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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128 }
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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129
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130 my $fn_out = "$tmp_dir/$tag.vcf";
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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131 my $fn_cons = "$tmp_dir/$tag.fasta";
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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132
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133 my @cmd_local = @cmd;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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134 push @cmd_local, '--window', $tag;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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135 push @cmd_local, '--outfile', $fn_out;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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136 push @cmd_local, '--consensus', $fn_cons;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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137
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138 my $ret = system @cmd_local;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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139
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jdv
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140 my $cmd_string = join ' ', @cmd_local;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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141 die "Non-zero exit value for command: $cmd_string\n"
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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142 if ($ret);
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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143
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144 }
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145
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146 }