Mercurial > repos > jdv > nanopolish

annotate nanopolish_variants.pl @ 11:550ac6458c07 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
author jdv
date Fri, 09 Mar 2018 21:50:06 -0500
parents c00a942cfc0b
children
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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
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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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
jdv
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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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550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
jdv
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7 use autodie;
550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
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550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
jdv
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9 use BioX::Seq::Stream;
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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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10 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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11 use File::Copy qw/copy/;
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550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
jdv
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12 use File::Temp qw/tempdir/;
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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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13 use Getopt::Long qw/:config pass_through/;
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b437c0a7ca04 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 419298c744d71488d78e1dadb868a4d8b933618e
jdv
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14 use List::Util qw/min/;
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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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15 use threads;
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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16 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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2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
jdv
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18 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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19 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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20 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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21 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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22 my $fn_fast5;
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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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23 my $fn_reads;
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24 my $fn_index;
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25 my $fn_bam;
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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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2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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27 # remember full command string (with proper binary)
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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29 # 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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30 GetOptions(
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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31 '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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32 '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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33 'outfile=s' => \$fn_outfile,
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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34 '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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35 'fast5=s' => \$fn_fast5,
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36 'reads=s' => \$fn_reads,
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37 'index=s' => \$fn_index,
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38 'bam=s' => \$fn_bam,
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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 );
2136c2725fc4 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
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41 my $ret;
bdd6c1ab07c5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 83364d7d78ca5524a08065daef995bfcd54a379d
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42
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550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
jdv
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43 my $cwd = abs_path( getcwd() );
550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
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44
550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
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45 $fn_genome = abs_path( $fn_genome ) if ( defined $fn_genome );
550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
jdv
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46 $fn_outfile = abs_path( $fn_outfile ) if ( defined $fn_outfile );
550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
jdv
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47 $fn_consensus = abs_path( $fn_consensus ) if ( defined $fn_consensus );
550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
jdv
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48 $fn_fast5 = abs_path( $fn_fast5 ) if ( defined $fn_fast5 );
550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
jdv
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49 $fn_reads = abs_path( $fn_reads ) if ( defined $fn_reads );
550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
jdv
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50 $fn_index = abs_path( $fn_index ) if ( defined $fn_index );
550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
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51
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52 # BAM filename is already symbolic link, so abs_path() won't work properly.
550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
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53 # What we actually want are new symbolic links to the same targets
550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
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54 my $fn_bai = $fn_bam;
550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
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55 $fn_bai =~ s/\.bam$/.bai/
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56 or die "Failed to replace extension of BAM index file";
550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
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57 my $bam_tgt = readlink $fn_bam;
550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
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58 my $bai_tgt = readlink $fn_bai;
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60 my $tmpdir = tempdir( CLEANUP => 1 );
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62 chdir $tmpdir;
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63 mkdir 'tmp';
550ac6458c07 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 3a5673ca0300ee8853958d854d9f433e9600944e
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64 symlink $bam_tgt, 'input.bam';
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65 symlink $bai_tgt, 'input.bai';
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66
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67 my $fn_link = 'reads';
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68
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69 # divide available threads between actual threads and regions
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70 #
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71 # 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
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72 # remaining threads for running parallel regions
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73 my $n_threads = min( 4, $threads );
b437c0a7ca04 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 419298c744d71488d78e1dadb868a4d8b933618e
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74 my $n_workers = int($threads/$n_threads);
b437c0a7ca04 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 419298c744d71488d78e1dadb868a4d8b933618e
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75
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76
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77 # extract FAST5 files to path where they are expected
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78 # use system 'tar' to transparently and safely handle absolute paths
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79 my $fast5_dir = 'fast5';
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80 mkdir $fast5_dir;
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81 chdir $fast5_dir;
4
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82 $ret = system(
bdd6c1ab07c5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 83364d7d78ca5524a08065daef995bfcd54a379d
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83 'tar',
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84 '-xf',
4
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85 $fn_fast5
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86 );
bdd6c1ab07c5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 83364d7d78ca5524a08065daef995bfcd54a379d
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87 die "Failed to extract tarball: $!\n"
bdd6c1ab07c5 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 83364d7d78ca5524a08065daef995bfcd54a379d
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88 if ($ret);
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89 chdir $tmpdir;
0
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90
7
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91 symlink( $fn_reads, $fn_link )
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92 or die "Failed to create symlink";
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93
3
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parents: 0
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94
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95 # index reads
7
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96 if (defined $fn_index) {
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97 $ret = system(
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98 'tar',
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99 '-xf',
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100 $fn_index
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101 );
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102 die "Failed to extract tarball: $!\n"
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103 if ($ret);
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104 }
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105 else {
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106 $ret = system(
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107 'nanopolish',
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108 'index',
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109 '--directory' => $fast5_dir,
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110 $fn_link,
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111 );
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112 die "Failed nanopolish indexing: $!\n"
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113 if ($ret);
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114 }
3
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115
0
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116 my @cmd = @ARGV;
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117 unshift @cmd, 'nanopolish';
8
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118 push @cmd, '--genome', $fn_genome;
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119 push @cmd, '--reads', $fn_link;
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120 push @cmd, '--threads', $n_threads;
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121 push @cmd, '--bam', 'input.bam';
0
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122
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123 my @regions :shared;
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124
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125 # build region tags to pass to nanopolish
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126 if (-s $fn_genome) { # gracefully handle empty inputs
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127 my $parser = BioX::Seq::Stream->new($fn_genome);
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128 while (my $seq = $parser->next_seq) {
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129 push @regions, join( ':', $seq->id,
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130 join( '-', 1, length($seq) ),
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131 );
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132 }
0
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133 }
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134
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135 my @workers;
8
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136 for (1..$n_workers) {
0
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137 push @workers, threads->create(\&run);
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138 }
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139
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140 $_->join() for (@workers);
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141
11
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142 my @fa_files = glob "tmp/*.fasta";
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143 my @out_files = glob "tmp/*.vcf";
0
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144
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145 open my $out_cons, '>', $fn_consensus
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146 or die "Failed to open output consensus: $!";
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147 for (@fa_files) {
9
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148 my $parser = BioX::Seq::Stream->new($_);
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149 while (my $seq = $parser->next_seq) {
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150 $seq->id =~ s/^.+\K:\d+-\d+$//; # strip coordinates from ID
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151 print {$out_cons} $seq->as_fasta;
0
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152 }
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153 }
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154 close $out_cons;
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155
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156 # we may need to do extra processing on VCF output
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157 open my $out_vcf, '>', $fn_outfile
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158 or die "Failed to open output file: $!";
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parents:
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159 for my $i (0..$#out_files) {
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160 my $v = $out_files[$i];
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161 open my $in, '<', $v;
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parents:
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162 while (my $line = <$in>) {
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163 next if ($line =~ /^\s*#/ && $i > 0);
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164 print {$out_vcf} $line;
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165 }
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parents:
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166 close $in;
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167 }
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168 close $out_vcf;
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169
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170
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171 sub run {
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172
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173 LOOP:
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174 while (1) {
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175
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176 my $tag;
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177
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178 {
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179 lock @regions;
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180 last LOOP if (! scalar @regions);
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181 $tag = shift @regions;
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182 }
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183
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184 my $fn_out = "tmp/$tag.vcf";
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185 my $fn_cons = "tmp/$tag.fasta";
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187 my @cmd_local = @cmd;
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188 push @cmd_local, '--window', $tag;
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189 push @cmd_local, '--outfile', $fn_out;
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190 push @cmd_local, '--consensus', $fn_cons;
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192 my $ret = system @cmd_local;
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194 my $cmd_string = join ' ', @cmd_local;
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195 die "Non-zero exit value for command: $cmd_string\n"
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196 if ($ret);
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198 }
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200 }