Mercurial > repos > jdv > nanopolish

annotate nanopolish_variants.pl @ 7:32cb27adeb34 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
author jdv
date Mon, 12 Feb 2018 00:58:10 -0500
parents bdd6c1ab07c5
children b437c0a7ca04
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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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20 my $fn_index;
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21
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22 # remember full command string (with proper binary)
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23
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24 # parse genome filename and add back to arg stack
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25 GetOptions(
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26 'genome=s' => \$fn_genome,
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27 'threads=i' => \$threads,
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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 'index=s' => \$fn_index,
0
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33 );
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34
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35 my $ret;
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36
7
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37 my $fn_link = 'reads';
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38 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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39 mkdir $tmp_dir;
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40
3
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41 $fn_fast5 = abs_path($fn_fast5);
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42
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43 # extract FAST5 files to path where they are expected
4
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44 # use system 'tar' to transparently and safely handle absolute paths
3
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45 my $fast5_dir = 'fast5';
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46 mkdir $fast5_dir;
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47 my $cwd = abs_path( getcwd() );
3
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48 chdir $fast5_dir;
4
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49 $ret = system(
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50 'tar',
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51 '-xf',
4
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52 $fn_fast5
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53 );
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54 die "Failed to extract tarball: $!\n"
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55 if ($ret);
0
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56 chdir $cwd;
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57
7
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58 symlink( $fn_reads, $fn_link )
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59 or die "Failed to create symlink";
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60
3
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61
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62 # index reads
7
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63 if (defined $fn_index) {
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64 $ret = system(
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65 'tar',
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66 '-xf',
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67 $fn_index
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68 );
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69 die "Failed to extract tarball: $!\n"
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70 if ($ret);
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71 }
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72 else {
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73 $ret = system(
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74 'nanopolish',
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75 'index',
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76 '--directory' => $fast5_dir,
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77 $fn_link,
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78 );
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79 die "Failed nanopolish indexing: $!\n"
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80 if ($ret);
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81 }
3
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82
0
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83 my @cmd = @ARGV;
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84 unshift @cmd, 'nanopolish';
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85 push @cmd, '--genome', $fn_genome;
7
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86 push @cmd, '--reads', $fn_link;
0
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87
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88 my @regions :shared;
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89
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90 # build region tags to pass to nanopolish
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91 my $parser = BioX::Seq::Stream->new($fn_genome);
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92 while (my $seq = $parser->next_seq) {
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93 push @regions, join( ':', $seq->id,
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94 join( '-', 1, length($seq) ),
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95 );
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96 }
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97
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98 my @workers;
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99 for (1..$threads) {
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100 push @workers, threads->create(\&run);
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101 }
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102
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103 $_->join() for (@workers);
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104
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105 my @fa_files = glob "$tmp_dir/*.fasta";
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106 my @out_files = glob "$tmp_dir/*.vcf";
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107
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108 open my $out_cons, '>', $fn_consensus
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109 or die "Failed to open output consensus: $!";
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110 for (@fa_files) {
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111 open my $in, '<', $_;
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112 while (my $line = <$in>) {
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113 print {$out_cons} $line;
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114 }
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115 close $in;
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116 }
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117 close $out_cons;
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118
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119 # we may need to do extra processing on VCF output
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120 open my $out_vcf, '>', $fn_outfile
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121 or die "Failed to open output file: $!";
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122 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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123 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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124 open my $in, '<', $v;
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125 while (my $line = <$in>) {
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126 next if ($line =~ /^\s*#/ && $i > 0);
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127 print {$out_vcf} $line;
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128 }
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129 close $in;
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130 }
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131 close $out_vcf;
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132
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133
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134 sub run {
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135
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136 LOOP:
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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137 while (1) {
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138
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139 my $tag;
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140
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141 {
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142 lock @regions;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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143 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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144 $tag = shift @regions;
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145 }
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146
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147 my $fn_out = "$tmp_dir/$tag.vcf";
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148 my $fn_cons = "$tmp_dir/$tag.fasta";
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149
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diff changeset
150 my @cmd_local = @cmd;
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151 push @cmd_local, '--window', $tag;
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152 push @cmd_local, '--outfile', $fn_out;
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153 push @cmd_local, '--consensus', $fn_cons;
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154
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155 my $ret = system @cmd_local;
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156
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157 my $cmd_string = join ' ', @cmd_local;
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158 die "Non-zero exit value for command: $cmd_string\n"
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159 if ($ret);
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160
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161 }
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162
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163 }