Mercurial > repos > jdv > nanopolish

annotate nanopolish_index.pl @ 8:b437c0a7ca04 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 419298c744d71488d78e1dadb868a4d8b933618e
author jdv
date Mon, 12 Feb 2018 03:06:42 -0500
parents 32cb27adeb34
children f64b148e6189
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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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2
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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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6
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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7 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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8 use File::Copy qw/copy/;
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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9 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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10 use threads;
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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11 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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12 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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13
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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14 my $fn_link = 'reads';
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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15
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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16 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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17 my $fn_reads;
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18 my $fn_outfile;
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19
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20 # parse genome filename and add back to arg stack
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21 GetOptions(
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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22 '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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23 'reads=s' => \$fn_reads,
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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24 'outfile=s' => \$fn_outfile,
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25 );
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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26
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27 my $ret;
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28
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29 $fn_fast5 = abs_path($fn_fast5);
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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30 $fn_reads = abs_path($fn_reads);
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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31 $fn_outfile = abs_path($fn_outfile);
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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32
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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33 # 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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34 my $fast5_dir = 'fast5';
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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35 if (-e $fast5_dir) {
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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36 warn "$fast5_dir exists, won't overwrite";
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37 exit;
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38 }
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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39 mkdir $fast5_dir;
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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40 my $cwd = abs_path( getcwd() );
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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41 chdir $fast5_dir;
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42
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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43 # use system 'tar' to transparently and safely handle absolute paths
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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44 $ret = system(
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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45 'tar',
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46 '-xf',
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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47 $fn_fast5
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48 );
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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49 die "Failed to extract tarball: $!\n"
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50 if ($ret);
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51
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52 chdir $cwd;
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53
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54 symlink( $fn_reads, $fn_link )
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55 or die "Failed to create symlink: $@";
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56
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57 # index reads
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58 $ret = system(
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59 'nanopolish',
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60 'index',
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61 '--directory' => $fast5_dir,
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62 $fn_link,
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63 );
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64 die "Failed nanopolish indexing: $!\n"
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65 if ($ret);
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66
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67 my @idx_fns = glob "$fn_link.*";
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68 $ret = system(
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69 'tar',
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70 '-cf' => $fn_outfile,
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71 @idx_fns,
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72 );
32cb27adeb34 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
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73 die "Failed tarball creation: $!\n"
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74 if ($ret);