/tools/next_gen_conversion/bwa_solid2fastq_modified.pl
https://bitbucket.org/h_morita_dbcls/galaxy-central · Perl · 89 lines · 77 code · 8 blank · 4 comment · 26 complexity · 8130b472aae8d09d7f96e7698dea606c MD5 · raw file
- #!/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) : ();
- }