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comparison pyPRADA_1.2/tools/bwa-0.5.7-mh/solid2fastq.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 # Author: lh3
4 # Note: Ideally, this script should be written in C. It is a bit slow at present.
5 # Also note that this script is different from the one contained in MAQ.
6
7 use strict;
8 use warnings;
9 use Getopt::Std;
10
11 my %opts;
12 my $version = '0.1.3';
13 my $usage = qq{
14 Usage: solid2fastq.pl <in.title> <out.prefix>
15
16 Note: <in.title> is the string showed in the `# Title:' line of a
17 ".csfasta" read file. Then <in.title>F3.csfasta is read sequence
18 file and <in.title>F3_QV.qual is the quality file. If
19 <in.title>R3.csfasta is present, this script assumes reads are
20 paired; otherwise reads will be regarded as single-end.
21
22 The read name will be <out.prefix>:panel_x_y/[12] with `1' for R3
23 tag and `2' for F3. Usually you may want to use short <out.prefix>
24 to save diskspace. Long <out.prefix> also causes troubles to maq.
25
26 };
27
28 getopts('', \%opts);
29 die($usage) if (@ARGV != 2);
30 my ($title, $pre) = @ARGV;
31 my (@fhr, @fhw);
32 my @fn_suff = ('F3.csfasta', 'F3_QV.qual', 'R3.csfasta', 'R3_QV.qual');
33 my $is_paired = (-f "$title$fn_suff[2]" || -f "$title$fn_suff[2].gz")? 1 : 0;
34 if ($is_paired) { # paired end
35 for (0 .. 3) {
36 my $fn = "$title$fn_suff[$_]";
37 $fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz");
38 open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n");
39 }
40 open($fhw[0], "|gzip >$pre.read2.fastq.gz") || die; # this is NOT a typo
41 open($fhw[1], "|gzip >$pre.read1.fastq.gz") || die;
42 open($fhw[2], "|gzip >$pre.single.fastq.gz") || die;
43 my (@df, @dr);
44 @df = &read1(1); @dr = &read1(2);
45 while (@df && @dr) {
46 if ($df[0] eq $dr[0]) { # mate pair
47 print {$fhw[0]} $df[1]; print {$fhw[1]} $dr[1];
48 @df = &read1(1); @dr = &read1(2);
49 } else {
50 if ($df[0] le $dr[0]) {
51 print {$fhw[2]} $df[1];
52 @df = &read1(1);
53 } else {
54 print {$fhw[2]} $dr[1];
55 @dr = &read1(2);
56 }
57 }
58 }
59 if (@df) {
60 print {$fhw[2]} $df[1];
61 while (@df = &read1(1, $fhr[0], $fhr[1])) {
62 print {$fhw[2]} $df[1];
63 }
64 }
65 if (@dr) {
66 print {$fhw[2]} $dr[1];
67 while (@dr = &read1(2, $fhr[2], $fhr[3])) {
68 print {$fhw[2]} $dr[1];
69 }
70 }
71 close($fhr[$_]) for (0 .. $#fhr);
72 close($fhw[$_]) for (0 .. $#fhw);
73 } else { # single end
74 for (0 .. 1) {
75 my $fn = "$title$fn_suff[$_]";
76 $fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz");
77 open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n");
78 }
79 open($fhw[2], "|gzip >$pre.single.fastq.gz") || die;
80 my @df;
81 while (@df = &read1(1, $fhr[0], $fhr[1])) {
82 print {$fhw[2]} $df[1];
83 }
84 close($fhr[$_]) for (0 .. $#fhr);
85 close($fhw[2]);
86 }
87
88 sub read1 {
89 my $i = shift(@_);
90 my $j = ($i-1)<<1;
91 my ($key, $seq);
92 my ($fhs, $fhq) = ($fhr[$j], $fhr[$j|1]);
93 while (<$fhs>) {
94 my $t = <$fhq>;
95 if (/^>(\d+)_(\d+)_(\d+)_[FR]3/) {
96 $key = sprintf("%.4d_%.4d_%.4d", $1, $2, $3); # this line could be improved on 64-bit machines
97 die(qq/** unmatched read name: '$_' != '$_'\n/) unless ($_ eq $t);
98 my $name = "$pre:$1_$2_$3/$i";
99 $_ = substr(<$fhs>, 2);
100 tr/0123./ACGTN/;
101 my $s = $_;
102 $_ = <$fhq>;
103 s/^(\d+)\s*//;
104 s/-1\b/0/eg;
105 s/(\d+)\s*/chr($1+33)/eg;
106 $seq = qq/\@$name\n$s+\n$_\n/;
107 last;
108 }
109 }
110 return defined($seq)? ($key, $seq) : ();
111 }