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comparison tools/next_gen_conversion/bwa_solid2fastq_modified.pl @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 #!/usr/bin/perl -w
2
3 # Author: lh3
4 # Note: Ideally, this script should be written in C. It is a bit slow at present.
5
6 use strict;
7 use warnings;
8 use Getopt::Std;
9
10 my %opts;
11 my $version = '0.1.3';
12 my $usage = qq{
13 Usage: solid2fastq.pl <paired> <outfile1> <outfile2> <F3.csfasta> <F3.qual> <R3.csfasta> <R3.qual>
14
15 Note: <in.title> is the string showed in the `# Title:' line of a
16 ".csfasta" read file. Then <in.title>F3.csfasta is read sequence
17 file and <in.title>F3_QV.qual is the quality file. If
18 <in.title>R3.csfasta is present, this script assumes reads are
19 paired; otherwise reads will be regarded as single-end.
20
21 The read name will be <out.prefix>:panel_x_y/[12] with `1' for R3
22 tag and `2' for F3. Usually you may want to use short <out.prefix>
23 to save diskspace. Long <out.prefix> also causes troubles to maq.
24
25 };
26
27 getopts('', \%opts);
28 die($usage) if (@ARGV != 7);
29 my ($is_paired,$outfile1,$outfile2,$f3reads,$f3qual,$r3reads,$r3qual) = @ARGV;
30 my (@fhr, @fhw);
31 my $fn = '';
32 my @fn_suff = ($f3reads,$f3qual,$r3reads,$r3qual);
33 if ($is_paired eq "yes") { # paired end
34 for (0 .. 3) {
35 $fn = $fn_suff[$_];
36 $fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz");
37 open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n");
38 }
39 open($fhw[0], "|gzip >$outfile2") || die;
40 open($fhw[1], "|gzip >$outfile1") || die;
41 my (@df, @dr);
42 @df = &read1(1); @dr = &read1(2);
43 while (@df && @dr) {
44 if ($df[0] eq $dr[0]) { # mate pair
45 print {$fhw[0]} $df[1]; print {$fhw[1]} $dr[1];
46 @df = &read1(1); @dr = &read1(2);
47 }
48 }
49 close($fhr[$_]) for (0 .. $#fhr);
50 close($fhw[$_]) for (0 .. $#fhw);
51 } else { # single end
52 for (0 .. 1) {
53 my $fn = "$fn_suff[$_]";
54 $fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz");
55 open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n");
56 }
57 open($fhw[2], "|gzip >$outfile1") || die;
58 my @df;
59 while (@df = &read1(1, $fhr[0], $fhr[1])) {
60 print {$fhw[2]} $df[1];
61 }
62 close($fhr[$_]) for (0 .. $#fhr);
63 close($fhw[2]);
64 }
65
66 sub read1 {
67 my $i = shift(@_);
68 my $j = ($i-1)<<1;
69 my ($key, $seq);
70 my ($fhs, $fhq) = ($fhr[$j], $fhr[$j|1]);
71 while (<$fhs>) {
72 my $t = <$fhq>;
73 if (/^>(\d+)_(\d+)_(\d+)_[FR]3/) {
74 $key = sprintf("%.4d_%.4d_%.4d", $1, $2, $3); # this line could be improved on 64-bit machines
75 #print $key;
76 die(qq/** unmatched read name: '$_' != '$t'\n/) unless ($_ eq $t);
77 my $name = "$1_$2_$3/$i";
78 $_ = substr(<$fhs>, 2);
79 tr/0123./ACGTN/;
80 my $s = $_;
81 $_ = <$fhq>;
82 s/^(\d+)\s*//;
83 s/(\d+)\s*/chr($1+33)/eg;
84 $seq = qq/\@$name\n$s+\n$_\n/;
85 last;
86 }
87 }
88 return defined($seq)? ($key, $seq) : ();
89 }