Mercurial > repos > jdv > nanopolish

annotate nanopolish_index.pl @ 12:f64b148e6189 draft default tip

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit ba4c46d7717e3acd346c9c6bf0bbc9bbecccc190
author jdv
date Fri, 09 Mar 2018 21:56:08 -0500
parents 32cb27adeb34
children
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32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
jdv
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1 #!/usr/bin/env perl
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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3 use strict;
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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4 use warnings;
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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5 use 5.012;
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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f64b148e6189 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit ba4c46d7717e3acd346c9c6bf0bbc9bbecccc190
jdv
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7 use autodie;
f64b148e6189 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit ba4c46d7717e3acd346c9c6bf0bbc9bbecccc190
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8
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9 use Cwd qw/getcwd abs_path/;
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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10 use File::Copy qw/copy/;
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f64b148e6189 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit ba4c46d7717e3acd346c9c6bf0bbc9bbecccc190
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11 use File::Temp qw/tempdir/;
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12 use Getopt::Long qw/:config pass_through/;
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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13 use threads;
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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14 use threads::shared;
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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15 use BioX::Seq::Stream;
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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17 my $fn_link = 'reads';
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19 my $fn_fast5;
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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20 my $fn_reads;
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21 my $fn_outfile;
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23 # parse genome filename and add back to arg stack
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24 GetOptions(
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
jdv
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25 'fast5=s' => \$fn_fast5,
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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26 'reads=s' => \$fn_reads,
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27 'outfile=s' => \$fn_outfile,
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28 );
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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30 my $ret;
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f64b148e6189 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit ba4c46d7717e3acd346c9c6bf0bbc9bbecccc190
jdv
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32 my $cwd = abs_path( getcwd() );
f64b148e6189 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit ba4c46d7717e3acd346c9c6bf0bbc9bbecccc190
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34 $fn_fast5 = abs_path($fn_fast5);
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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35 $fn_reads = abs_path($fn_reads);
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36 $fn_outfile = abs_path($fn_outfile);
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38 my $tmpdir = tempdir( CLEANUP => 1 );
f64b148e6189 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit ba4c46d7717e3acd346c9c6bf0bbc9bbecccc190
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40 chdir $tmpdir;
f64b148e6189 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit ba4c46d7717e3acd346c9c6bf0bbc9bbecccc190
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41
7
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42 # extract FAST5 files to path where they are expected
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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43 my $fast5_dir = 'fast5';
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44 if (-e $fast5_dir) {
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45 warn "$fast5_dir exists, won't overwrite";
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46 exit;
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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47 }
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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48 mkdir $fast5_dir;
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49 chdir $fast5_dir;
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50
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51 # use system 'tar' to transparently and safely handle absolute paths
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52 $ret = system(
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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53 'tar',
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54 '-xf',
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55 $fn_fast5
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56 );
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57 die "Failed to extract tarball: $!\n"
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58 if ($ret);
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59
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60 chdir $tmpdir;
7
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61
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62 symlink( $fn_reads, $fn_link )
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63 or die "Failed to create symlink: $@";
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64
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65 # index reads
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66 $ret = system(
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67 'nanopolish',
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68 'index',
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69 '--directory' => $fast5_dir,
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70 $fn_link,
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71 );
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72 die "Failed nanopolish indexing: $!\n"
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73 if ($ret);
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74
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75 my @idx_fns = glob "$fn_link.*";
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76 $ret = system(
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77 'tar',
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78 '-cf' => $fn_outfile,
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79 @idx_fns,
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80 );
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81 die "Failed tarball creation: $!\n"
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82 if ($ret);