Mercurial > repos > jdv > nanopolish

annotate nanopolish_variants.pl @ 3:a1d433401bc2 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit e9238df905c413aaab086ea146cb1b97e3ffa0fd
author jdv
date Sat, 14 Oct 2017 00:05:43 -0400
parents 2136c2725fc4
children bdd6c1ab07c5
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2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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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;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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6
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7 use Archive::Tar;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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8 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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9 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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10 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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11 use threads;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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12 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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13 use BioX::Seq::Stream;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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14
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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15 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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16 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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17 my $fn_outfile;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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18 my $fn_consensus;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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19 my $fn_fast5;
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20 my $fn_reads;
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21
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22 # remember full command string (with proper binary)
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24 # parse genome filename and add back to arg stack
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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25 GetOptions(
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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26 'genome=s' => \$fn_genome,
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27 'threads=i' => \$threads,
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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28 'outfile=s' => \$fn_outfile,
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29 'consensus=s' => \$fn_consensus,
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30 'fast5=s' => \$fn_fast5,
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31 'reads=s' => \$fn_reads,
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32 );
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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33
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34 my $tmp_dir = 'tmp_dir';
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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35 mkdir $tmp_dir;
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36
3
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37 $fn_fast5 = abs_path($fn_fast5);
a1d433401bc2 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit e9238df905c413aaab086ea146cb1b97e3ffa0fd
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38
a1d433401bc2 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit e9238df905c413aaab086ea146cb1b97e3ffa0fd
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39 # extract FAST5 files to path where they are expected
a1d433401bc2 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit e9238df905c413aaab086ea146cb1b97e3ffa0fd
jdv
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40 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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41 mkdir $fast5_dir;
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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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42 my $cwd = abs_path( getcwd() );
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a1d433401bc2 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit e9238df905c413aaab086ea146cb1b97e3ffa0fd
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43 chdir $fast5_dir;
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44 my $tar = Archive::Tar->new();
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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45 $tar->read($fn_fast5);
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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46 $tar->extract();
3
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47 say "done extracting $fn_fast5 here";
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48 chdir $cwd;
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49
3
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50
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51 # index reads
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52 my $ret = system(
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53 'nanopolish',
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54 'index',
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55 '--directory' => $fast5_dir,
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56 $fn_reads,
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57 );
a1d433401bc2 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit e9238df905c413aaab086ea146cb1b97e3ffa0fd
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58 die "Failed nanopolish indexing: $!\n"
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59 if ($ret);
a1d433401bc2 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit e9238df905c413aaab086ea146cb1b97e3ffa0fd
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60
0
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61 my @cmd = @ARGV;
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62 unshift @cmd, 'nanopolish';
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63 push @cmd, '--genome', $fn_genome;
3
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64 push @cmd, '--reads', $fn_reads;
0
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65
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66 my @regions :shared;
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67
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68 # build region tags to pass to nanopolish
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69 my $parser = BioX::Seq::Stream->new($fn_genome);
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70 while (my $seq = $parser->next_seq) {
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71 push @regions, join( ':', $seq->id,
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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72 join( '-', 1, length($seq) ),
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73 );
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74 }
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75
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76 my @workers;
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77 for (1..$threads) {
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78 push @workers, threads->create(\&run);
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79 }
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80
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81 $_->join() for (@workers);
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82
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83 my @fa_files = glob "$tmp_dir/*.fasta";
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84 my @out_files = glob "$tmp_dir/*.vcf";
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85
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86 open my $out_cons, '>', $fn_consensus
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87 or die "Failed to open output consensus: $!";
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88 for (@fa_files) {
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89 open my $in, '<', $_;
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90 while (my $line = <$in>) {
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91 print {$out_cons} $line;
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92 }
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93 close $in;
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94 }
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95 close $out_cons;
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96
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97 # we may need to do extra processing on VCF output
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98 open my $out_vcf, '>', $fn_outfile
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99 or die "Failed to open output file: $!";
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100 for my $i (0..$#out_files) {
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101 my $v = $out_files[$i];
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102 open my $in, '<', $v;
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103 while (my $line = <$in>) {
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104 next if ($line =~ /^\s*#/ && $i > 0);
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105 print {$out_vcf} $line;
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106 }
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107 close $in;
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108 }
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109 close $out_vcf;
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110
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111
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112 sub run {
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113
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114 LOOP:
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115 while (1) {
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116
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117 my $tag;
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118
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119 {
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120 lock @regions;
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121 last LOOP if (! scalar @regions);
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122 $tag = shift @regions;
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123 }
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124
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125 my $fn_out = "$tmp_dir/$tag.vcf";
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126 my $fn_cons = "$tmp_dir/$tag.fasta";
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127
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128 my @cmd_local = @cmd;
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129 push @cmd_local, '--window', $tag;
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130 push @cmd_local, '--outfile', $fn_out;
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131 push @cmd_local, '--consensus', $fn_cons;
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132
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133 my $ret = system @cmd_local;
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134
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135 my $cmd_string = join ' ', @cmd_local;
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136 die "Non-zero exit value for command: $cmd_string\n"
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137 if ($ret);
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138
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139 }
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140
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141 }