Mercurial > repos > ashvark > qiime_1_8_0
view bwa-0.6.2/qualfa2fq.pl @ 0:dd1186b11b3b draft
Uploaded BWA
author | ashvark |
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date | Fri, 18 Jul 2014 07:55:14 -0400 |
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#!/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);