Mercurial > repos > ashvark > qiime_1_8_0
diff bwa-0.6.2/qualfa2fq.pl @ 2:a294fbfcb1db draft default tip
Uploaded BWA
author | ashvark |
---|---|
date | Fri, 18 Jul 2014 07:55:59 -0400 |
parents | dd1186b11b3b |
children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwa-0.6.2/qualfa2fq.pl Fri Jul 18 07:55:59 2014 -0400 @@ -0,0 +1,27 @@ +#!/usr/bin/perl -w + +use strict; +use warnings; + +die("Usage: qualfa2fq.pl <in.fasta> <in.qual>\n") if (@ARGV != 2); + +my ($fhs, $fhq, $q); +open($fhs, ($ARGV[0] =~ /\.gz$/)? "gzip -dc $ARGV[0] |" : $ARGV[0]) || die; +open($fhq, ($ARGV[1] =~ /\.gz$/)? "gzip -dc $ARGV[1] |" : $ARGV[1]) || die; + +$/ = ">"; <$fhs>; <$fhq>; $/ = "\n"; +while (<$fhs>) { + $q = <$fhq>; + print "\@$_"; + $/ = ">"; + $_ = <$fhs>; $q = <$fhq>; + chomp; chomp($q); + $q =~ s/\s*(\d+)\s*/chr($1+33)/eg; + print $_, "+\n"; + for (my $i = 0; $i < length($q); $i += 60) { + print substr($q, $i, 60), "\n"; + } + $/ = "\n"; +} + +close($fhs); close($fhq);