Mercurial > repos > jdv > nanopolish

diff nanopolish_variants.pl @ 9:f1141f6a2d65 draft
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
--- a/nanopolish_variants.pl	Mon Feb 12 03:06:42 2018 -0500
+++ b/nanopolish_variants.pl	Mon Feb 12 23:15:26 2018 -0500
@@ -118,11 +118,11 @@
 open my $out_cons, '>', $fn_consensus
     or die "Failed to open output consensus: $!";
 for (@fa_files) {
-    open my $in, '<', $_;
-    while (my $line = <$in>) {
-        print {$out_cons} $line;
+    my $parser =  BioX::Seq::Stream->new($_);
+    while (my $seq = $parser->next_seq) {
+        $seq->id =~ s/^.+\K:\d+-\d+$//; # strip coordinates from ID
+        print {$out_cons} $seq->as_fasta;
     }
-    close $in;
 }
 close $out_cons;