Mercurial > repos > jdv > nanopolish

annotate nanopolish_variants.pl @ 10:c00a942cfc0b draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 1eeffb2cd0b8115ca185f7fcb2df2920dff33e3b
author jdv
date Mon, 12 Feb 2018 23:59:21 -0500
parents f1141f6a2d65
children 550ac6458c07
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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
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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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/;
8
b437c0a7ca04 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 419298c744d71488d78e1dadb868a4d8b933618e
jdv
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10 use List::Util qw/min/;
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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;
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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 my $fn_index;
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23 # remember full command string (with proper binary)
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24
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25 # 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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26 GetOptions(
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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27 'genome=s' => \$fn_genome,
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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28 '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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29 'outfile=s' => \$fn_outfile,
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30 'consensus=s' => \$fn_consensus,
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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31 'fast5=s' => \$fn_fast5,
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32 'reads=s' => \$fn_reads,
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33 'index=s' => \$fn_index,
0
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34 );
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35
4
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36 my $ret;
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37
7
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38 my $fn_link = 'reads';
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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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39 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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40 mkdir $tmp_dir;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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41
8
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42 # divide available threads between actual threads and regions
b437c0a7ca04 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 419298c744d71488d78e1dadb868a4d8b933618e
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43 #
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44 # testing suggests minimal speed-up past 4-8 actual threads per region, so use
b437c0a7ca04 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 419298c744d71488d78e1dadb868a4d8b933618e
jdv
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45 # remaining threads for running parallel regions
b437c0a7ca04 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 419298c744d71488d78e1dadb868a4d8b933618e
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46 my $n_threads = min( 4, $threads );
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47 my $n_workers = int($threads/$n_threads);
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48
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49
3
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50 $fn_fast5 = abs_path($fn_fast5);
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51
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52 # extract FAST5 files to path where they are expected
4
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53 # use system 'tar' to transparently and safely handle absolute paths
3
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54 my $fast5_dir = 'fast5';
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55 mkdir $fast5_dir;
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56 my $cwd = abs_path( getcwd() );
3
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57 chdir $fast5_dir;
4
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58 $ret = system(
bdd6c1ab07c5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 83364d7d78ca5524a08065daef995bfcd54a379d
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59 'tar',
7
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60 '-xf',
4
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61 $fn_fast5
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62 );
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63 die "Failed to extract tarball: $!\n"
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64 if ($ret);
0
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65 chdir $cwd;
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66
7
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67 symlink( $fn_reads, $fn_link )
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68 or die "Failed to create symlink";
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69
3
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70
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71 # index reads
7
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72 if (defined $fn_index) {
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73 $ret = system(
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74 'tar',
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75 '-xf',
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76 $fn_index
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77 );
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78 die "Failed to extract tarball: $!\n"
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79 if ($ret);
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80 }
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81 else {
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82 $ret = system(
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83 'nanopolish',
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84 'index',
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85 '--directory' => $fast5_dir,
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86 $fn_link,
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87 );
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88 die "Failed nanopolish indexing: $!\n"
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89 if ($ret);
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90 }
3
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91
0
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92 my @cmd = @ARGV;
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93 unshift @cmd, 'nanopolish';
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94 push @cmd, '--genome', $fn_genome;
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95 push @cmd, '--reads', $fn_link;
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96 push @cmd, '--threads', $n_threads;
0
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97
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98 my @regions :shared;
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99
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100 # build region tags to pass to nanopolish
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101 if (-s $fn_genome) { # gracefully handle empty inputs
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102 my $parser = BioX::Seq::Stream->new($fn_genome);
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103 while (my $seq = $parser->next_seq) {
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104 push @regions, join( ':', $seq->id,
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105 join( '-', 1, length($seq) ),
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106 );
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107 }
0
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108 }
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109
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110 my @workers;
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111 for (1..$n_workers) {
0
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112 push @workers, threads->create(\&run);
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113 }
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114
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115 $_->join() for (@workers);
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116
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117 my @fa_files = glob "$tmp_dir/*.fasta";
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118 my @out_files = glob "$tmp_dir/*.vcf";
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119
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120 open my $out_cons, '>', $fn_consensus
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121 or die "Failed to open output consensus: $!";
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122 for (@fa_files) {
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123 my $parser = BioX::Seq::Stream->new($_);
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124 while (my $seq = $parser->next_seq) {
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125 $seq->id =~ s/^.+\K:\d+-\d+$//; # strip coordinates from ID
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126 print {$out_cons} $seq->as_fasta;
0
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127 }
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128 }
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129 close $out_cons;
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130
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131 # we may need to do extra processing on VCF output
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132 open my $out_vcf, '>', $fn_outfile
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133 or die "Failed to open output file: $!";
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134 for my $i (0..$#out_files) {
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135 my $v = $out_files[$i];
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136 open my $in, '<', $v;
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137 while (my $line = <$in>) {
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138 next if ($line =~ /^\s*#/ && $i > 0);
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139 print {$out_vcf} $line;
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140 }
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141 close $in;
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142 }
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143 close $out_vcf;
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144
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145
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146 sub run {
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147
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148 LOOP:
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149 while (1) {
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150
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151 my $tag;
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152
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153 {
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154 lock @regions;
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155 last LOOP if (! scalar @regions);
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156 $tag = shift @regions;
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157 }
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158
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159 my $fn_out = "$tmp_dir/$tag.vcf";
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160 my $fn_cons = "$tmp_dir/$tag.fasta";
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161
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162 my @cmd_local = @cmd;
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163 push @cmd_local, '--window', $tag;
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164 push @cmd_local, '--outfile', $fn_out;
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165 push @cmd_local, '--consensus', $fn_cons;
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166
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167 my $ret = system @cmd_local;
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168
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169 my $cmd_string = join ' ', @cmd_local;
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170 die "Non-zero exit value for command: $cmd_string\n"
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171 if ($ret);
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172
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173 }
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174
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175 }