root/galaxy-central/tools/next_gen_conversion/bwa_solid2fastq_modified.pl @ 3

#!/usr/bin/perl -w

# Author: lh3
# Note: Ideally, this script should be written in C. It is a bit slow at present.

use strict;
use warnings;
use Getopt::Std;

my %opts;
my $version = '0.1.3';
my $usage = qq{
Usage: solid2fastq.pl <paired> <outfile1> <outfile2> <F3.csfasta> <F3.qual> <R3.csfasta> <R3.qual> 

Note: <in.title> is the string showed in the `# Title:' line of a
      ".csfasta" read file. Then <in.title>F3.csfasta is read sequence
      file and <in.title>F3_QV.qual is the quality file. If
      <in.title>R3.csfasta is present, this script assumes reads are
      paired; otherwise reads will be regarded as single-end.

      The read name will be <out.prefix>:panel_x_y/[12] with `1' for R3
      tag and `2' for F3. Usually you may want to use short <out.prefix>
      to save diskspace. Long <out.prefix> also causes troubles to maq.

};

getopts('', \%opts);
die($usage) if (@ARGV != 7);
my ($is_paired,$outfile1,$outfile2,$f3reads,$f3qual,$r3reads,$r3qual) = @ARGV;
my (@fhr, @fhw);
my $fn = '';
my @fn_suff = ($f3reads,$f3qual,$r3reads,$r3qual);
if ($is_paired eq "yes") { # paired end
  for (0 .. 3) {
        $fn = $fn_suff[$_];
        $fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz");
        open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n");
  }
  open($fhw[0], "|gzip >$outfile2") || die;
  open($fhw[1], "|gzip >$outfile1") || die;
  my (@df, @dr);
  @df = &read1(1); @dr = &read1(2);
  while (@df && @dr) {
        if ($df[0] eq $dr[0]) { # mate pair
          print {$fhw[0]} $df[1]; print {$fhw[1]} $dr[1];
          @df = &read1(1); @dr = &read1(2);
        }
  }
  close($fhr[$_]) for (0 .. $#fhr);
  close($fhw[$_]) for (0 .. $#fhw);
} else { # single end
  for (0 .. 1) {
        my $fn = "$fn_suff[$_]";
        $fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz");
        open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n");
  }
  open($fhw[2], "|gzip >$outfile1") || die;
  my @df;
  while (@df = &read1(1, $fhr[0], $fhr[1])) {
        print {$fhw[2]} $df[1];
  }
  close($fhr[$_]) for (0 .. $#fhr);
  close($fhw[2]);
}

sub read1 {
  my $i = shift(@_);
  my $j = ($i-1)<<1;
  my ($key, $seq);
  my ($fhs, $fhq) = ($fhr[$j], $fhr[$j|1]);
  while (<$fhs>) {
        my $t = <$fhq>;
        if (/^>(\d+)_(\d+)_(\d+)_[FR]3/) {
          $key = sprintf("%.4d_%.4d_%.4d", $1, $2, $3); # this line could be improved on 64-bit machines
          #print $key;
          die(qq/** unmatched read name: '$_' != '$t'\n/) unless ($_ eq $t);
          my $name = "$1_$2_$3/$i";
          $_ = substr(<$fhs>, 2);
          tr/0123./ACGTN/;
          my $s = $_;
          $_ = <$fhq>;
          s/^(\d+)\s*//;
          s/(\d+)\s*/chr($1+33)/eg;
          $seq = qq/\@$name\n$s+\n$_\n/;
          last;
        } 
  }
  return defined($seq)? ($key, $seq) : ();
}