/tools/next_gen_conversion/bwa_solid2fastq_modified.pl

 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
 6use strict;
 7use warnings;
 8use Getopt::Std;
 9
10my %opts;
11my $version = '0.1.3';
12my $usage = qq{
13Usage: solid2fastq.pl <paired> <outfile1> <outfile2> <F3.csfasta> <F3.qual> <R3.csfasta> <R3.qual> 
14
15Note: <in.title> is the string showed in the `# Title:' line of a
16      ".csfasta" read file. Then <in.title>F3.csfasta is read sequence
17      file and <in.title>F3_QV.qual is the quality file. If
18      <in.title>R3.csfasta is present, this script assumes reads are
19      paired; otherwise reads will be regarded as single-end.
20
21      The read name will be <out.prefix>:panel_x_y/[12] with `1' for R3
22      tag and `2' for F3. Usually you may want to use short <out.prefix>
23      to save diskspace. Long <out.prefix> also causes troubles to maq.
24
25};
26
27getopts('', \%opts);
28die($usage) if (@ARGV != 7);
29my ($is_paired,$outfile1,$outfile2,$f3reads,$f3qual,$r3reads,$r3qual) = @ARGV;
30my (@fhr, @fhw);
31my $fn = '';
32my @fn_suff = ($f3reads,$f3qual,$r3reads,$r3qual);
33if ($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
66sub 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}