Mercurial > repos > jdv > nanopolish

comparison nanopolish_variants.pl @ 9:f1141f6a2d65 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0ace87b59137f1ed770db97fbb33036e16205edf
author jdv
date Mon, 12 Feb 2018 23:15:26 -0500
parents b437c0a7ca04
children c00a942cfc0b
comparison
equal deleted inserted replaced
8:b437c0a7ca04 9:f1141f6a2d65
116 my @out_files = glob "$tmp_dir/*.vcf"; 116 my @out_files = glob "$tmp_dir/*.vcf";
117 117
118 open my $out_cons, '>', $fn_consensus 118 open my $out_cons, '>', $fn_consensus
119 or die "Failed to open output consensus: $!"; 119 or die "Failed to open output consensus: $!";
120 for (@fa_files) { 120 for (@fa_files) {
121 open my $in, '<', $_; 121 my $parser = BioX::Seq::Stream->new($_);
122 while (my $line = <$in>) { 122 while (my $seq = $parser->next_seq) {
123 print {$out_cons} $line; 123 $seq->id =~ s/^.+\K:\d+-\d+$//; # strip coordinates from ID
124 print {$out_cons} $seq->as_fasta;
124 } 125 }
125 close $in;
126 } 126 }
127 close $out_cons; 127 close $out_cons;
128 128
129 # we may need to do extra processing on VCF output 129 # we may need to do extra processing on VCF output
130 open my $out_vcf, '>', $fn_outfile 130 open my $out_vcf, '>', $fn_outfile