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comparison pyPRADA_1.2/tools/bwa-0.5.7-mh/qualfa2fq.pl @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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-1:000000000000 0:acc2ca1a3ba4
1 #!/usr/bin/perl -w
2
3 use strict;
4 use warnings;
5
6 die("Usage: qualfa2fq.pl <in.fasta> <in.qual>\n") if (@ARGV != 2);
7
8 my ($fhs, $fhq, $q);
9 open($fhs, ($ARGV[0] =~ /\.gz$/)? "gzip -dc $ARGV[0] |" : $ARGV[0]) || die;
10 open($fhq, ($ARGV[1] =~ /\.gz$/)? "gzip -dc $ARGV[1] |" : $ARGV[1]) || die;
11
12 $/ = ">"; <$fhs>; <$fhq>; $/ = "\n";
13 while (<$fhs>) {
14 $q = <$fhq>;
15 print "\@$_";
16 $/ = ">";
17 $_ = <$fhs>; $q = <$fhq>;
18 chomp; chomp($q);
19 $q =~ s/\s*(\d+)\s*/chr($1+33)/eg;
20 print $_, "+\n";
21 for (my $i = 0; $i < length($q); $i += 60) {
22 print substr($q, $i, 60), "\n";
23 }
24 $/ = "\n";
25 }
26
27 close($fhs); close($fhq);