Mercurial > repos > siyuan > prada
comparison pyPRADA_1.2/tools/bwa-0.5.7-mh/qualfa2fq.pl @ 0:acc2ca1a3ba4
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author | siyuan |
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date | Thu, 20 Feb 2014 00:44:58 -0500 |
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-1:000000000000 | 0:acc2ca1a3ba4 |
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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); |