Mercurial > repos > jdv > nanopolish

comparison nanopolish_variants.pl @ 3:a1d433401bc2 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit e9238df905c413aaab086ea146cb1b97e3ffa0fd
author jdv
date Sat, 14 Oct 2017 00:05:43 -0400
parents 2136c2725fc4
children bdd6c1ab07c5
comparison
equal deleted inserted replaced
2:e4b6d4a53f2e 3:a1d433401bc2
15 my $fn_genome; 15 my $fn_genome;
16 my $threads = 1; 16 my $threads = 1;
17 my $fn_outfile; 17 my $fn_outfile;
18 my $fn_consensus; 18 my $fn_consensus;
19 my $fn_fast5; 19 my $fn_fast5;
20 my $fn_reads;
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(
25 'genome=s' => \$fn_genome, 26 'genome=s' => \$fn_genome,
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,
31 'reads=s' => \$fn_reads,
30 ); 32 );
31 33
32 my $tmp_dir = 'tmp_dir'; 34 my $tmp_dir = 'tmp_dir';
33 mkdir $tmp_dir; 35 mkdir $tmp_dir;
34 36
35 #extract FAST5 files to path where they are expected 37 $fn_fast5 = abs_path($fn_fast5);
36 my $in_dir = 'in_dir'; 38
37 mkdir $in_dir; 39 # extract FAST5 files to path where they are expected
40 my $fast5_dir = 'fast5';
41 mkdir $fast5_dir;
38 my $cwd = abs_path( getcwd() ); 42 my $cwd = abs_path( getcwd() );
39 chdir $in_dir; 43 chdir $fast5_dir;
40 my $tar = Archive::Tar->new(); 44 my $tar = Archive::Tar->new();
41 $tar->read($fn_fast5); 45 $tar->read($fn_fast5);
42 $tar->extract(); 46 $tar->extract();
47 say "done extracting $fn_fast5 here";
43 chdir $cwd; 48 chdir $cwd;
49
50
51 # index reads
52 my $ret = system(
53 'nanopolish',
54 'index',
55 '--directory' => $fast5_dir,
56 $fn_reads,
57 );
58 die "Failed nanopolish indexing: $!\n"
59 if ($ret);
44 60
45 my @cmd = @ARGV; 61 my @cmd = @ARGV;
46 unshift @cmd, 'nanopolish'; 62 unshift @cmd, 'nanopolish';
47 push @cmd, '--genome', $fn_genome; 63 push @cmd, '--genome', $fn_genome;
48 64 push @cmd, '--reads', $fn_reads;
49 say join ' ', @cmd;
50 65
51 my @regions :shared; 66 my @regions :shared;
52 67
53 # build region tags to pass to nanopolish 68 # build region tags to pass to nanopolish
54 my $parser = BioX::Seq::Stream->new($fn_genome); 69 my $parser = BioX::Seq::Stream->new($fn_genome);
114 push @cmd_local, '--window', $tag; 129 push @cmd_local, '--window', $tag;
115 push @cmd_local, '--outfile', $fn_out; 130 push @cmd_local, '--outfile', $fn_out;
116 push @cmd_local, '--consensus', $fn_cons; 131 push @cmd_local, '--consensus', $fn_cons;
117 132
118 my $ret = system @cmd_local; 133 my $ret = system @cmd_local;
119 warn "RET: $ret ($!)\n";
120 134
121 my $cmd_string = join ' ', @cmd_local; 135 my $cmd_string = join ' ', @cmd_local;
122 die "Non-zero exit value for command: $cmd_string\n" 136 die "Non-zero exit value for command: $cmd_string\n"
123 if ($ret); 137 if ($ret);
124 138