Mercurial > repos > jdv > nanopolish

comparison 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
comparison
equal deleted inserted replaced
6:36cc4ae4160e 7:32cb27adeb34
15 my $threads = 1; 15 my $threads = 1;
16 my $fn_outfile; 16 my $fn_outfile;
17 my $fn_consensus; 17 my $fn_consensus;
18 my $fn_fast5; 18 my $fn_fast5;
19 my $fn_reads; 19 my $fn_reads;
20 my $fn_index;
20 21
21 # remember full command string (with proper binary) 22 # remember full command string (with proper binary)
22 23
23 # parse genome filename and add back to arg stack 24 # parse genome filename and add back to arg stack
24 GetOptions( 25 GetOptions(
26 'threads=i' => \$threads, 27 'threads=i' => \$threads,
27 'outfile=s' => \$fn_outfile, 28 'outfile=s' => \$fn_outfile,
28 'consensus=s' => \$fn_consensus, 29 'consensus=s' => \$fn_consensus,
29 'fast5=s' => \$fn_fast5, 30 'fast5=s' => \$fn_fast5,
30 'reads=s' => \$fn_reads, 31 'reads=s' => \$fn_reads,
32 'index=s' => \$fn_index,
31 ); 33 );
32 34
33 my $ret; 35 my $ret;
34 36
37 my $fn_link = 'reads';
35 my $tmp_dir = 'tmp_dir'; 38 my $tmp_dir = 'tmp_dir';
36 mkdir $tmp_dir; 39 mkdir $tmp_dir;
37 40
38 $fn_fast5 = abs_path($fn_fast5); 41 $fn_fast5 = abs_path($fn_fast5);
39 42
43 mkdir $fast5_dir; 46 mkdir $fast5_dir;
44 my $cwd = abs_path( getcwd() ); 47 my $cwd = abs_path( getcwd() );
45 chdir $fast5_dir; 48 chdir $fast5_dir;
46 $ret = system( 49 $ret = system(
47 'tar', 50 'tar',
48 '-xvf', 51 '-xf',
49 $fn_fast5 52 $fn_fast5
50 ); 53 );
51 die "Failed to extract tarball: $!\n" 54 die "Failed to extract tarball: $!\n"
52 if ($ret); 55 if ($ret);
53 chdir $cwd; 56 chdir $cwd;
54 57
58 symlink( $fn_reads, $fn_link )
59 or die "Failed to create symlink";
60
55 61
56 # index reads 62 # index reads
57 $ret = system( 63 if (defined $fn_index) {
58 'nanopolish', 64 $ret = system(
59 'index', 65 'tar',
60 '--directory' => $fast5_dir, 66 '-xf',
61 $fn_reads, 67 $fn_index
62 ); 68 );
63 die "Failed nanopolish indexing: $!\n" 69 die "Failed to extract tarball: $!\n"
64 if ($ret); 70 if ($ret);
71 }
72 else {
73 $ret = system(
74 'nanopolish',
75 'index',
76 '--directory' => $fast5_dir,
77 $fn_link,
78 );
79 die "Failed nanopolish indexing: $!\n"
80 if ($ret);
81 }
65 82
66 my @cmd = @ARGV; 83 my @cmd = @ARGV;
67 unshift @cmd, 'nanopolish'; 84 unshift @cmd, 'nanopolish';
68 push @cmd, '--genome', $fn_genome; 85 push @cmd, '--genome', $fn_genome;
69 push @cmd, '--reads', $fn_reads; 86 push @cmd, '--reads', $fn_link;
70 87
71 my @regions :shared; 88 my @regions :shared;
72 89
73 # build region tags to pass to nanopolish 90 # build region tags to pass to nanopolish
74 my $parser = BioX::Seq::Stream->new($fn_genome); 91 my $parser = BioX::Seq::Stream->new($fn_genome);