Mercurial > repos > jdv > nanopolish

comparison nanopolish_variants.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 f1141f6a2d65
comparison
equal deleted inserted replaced
7:32cb27adeb34 8:b437c0a7ca04
5 use 5.012; 5 use 5.012;
6 6
7 use Cwd qw/getcwd abs_path/; 7 use Cwd qw/getcwd abs_path/;
8 use File::Copy qw/copy/; 8 use File::Copy qw/copy/;
9 use Getopt::Long qw/:config pass_through/; 9 use Getopt::Long qw/:config pass_through/;
10 use List::Util qw/min/;
10 use threads; 11 use threads;
11 use threads::shared; 12 use threads::shared;
12 use BioX::Seq::Stream; 13 use BioX::Seq::Stream;
13 14
14 my $fn_genome; 15 my $fn_genome;
35 my $ret; 36 my $ret;
36 37
37 my $fn_link = 'reads'; 38 my $fn_link = 'reads';
38 my $tmp_dir = 'tmp_dir'; 39 my $tmp_dir = 'tmp_dir';
39 mkdir $tmp_dir; 40 mkdir $tmp_dir;
41
42 # divide available threads between actual threads and regions
43 #
44 # testing suggests minimal speed-up past 4-8 actual threads per region, so use
45 # remaining threads for running parallel regions
46 my $n_threads = min( 4, $threads );
47 my $n_workers = int($threads/$n_threads);
48
40 49
41 $fn_fast5 = abs_path($fn_fast5); 50 $fn_fast5 = abs_path($fn_fast5);
42 51
43 # extract FAST5 files to path where they are expected 52 # extract FAST5 files to path where they are expected
44 # use system 'tar' to transparently and safely handle absolute paths 53 # use system 'tar' to transparently and safely handle absolute paths
80 if ($ret); 89 if ($ret);
81 } 90 }
82 91
83 my @cmd = @ARGV; 92 my @cmd = @ARGV;
84 unshift @cmd, 'nanopolish'; 93 unshift @cmd, 'nanopolish';
85 push @cmd, '--genome', $fn_genome; 94 push @cmd, '--genome', $fn_genome;
86 push @cmd, '--reads', $fn_link; 95 push @cmd, '--reads', $fn_link;
96 push @cmd, '--threads', $n_threads;
87 97
88 my @regions :shared; 98 my @regions :shared;
89 99
90 # build region tags to pass to nanopolish 100 # build region tags to pass to nanopolish
91 my $parser = BioX::Seq::Stream->new($fn_genome); 101 my $parser = BioX::Seq::Stream->new($fn_genome);
94 join( '-', 1, length($seq) ), 104 join( '-', 1, length($seq) ),
95 ); 105 );
96 } 106 }
97 107
98 my @workers; 108 my @workers;
99 for (1..$threads) { 109 for (1..$n_workers) {
100 push @workers, threads->create(\&run); 110 push @workers, threads->create(\&run);
101 } 111 }
102 112
103 $_->join() for (@workers); 113 $_->join() for (@workers);
104 114