112 lines
3.1 KiB
Perl
112 lines
3.1 KiB
Perl
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#!/usr/bin/perl -w
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# Author: lh3
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# Note: Ideally, this script should be written in C. It is a bit slow at present.
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# Also note that this script is different from the one contained in MAQ.
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use strict;
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use warnings;
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use Getopt::Std;
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my %opts;
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my $version = '0.1.4';
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my $usage = qq{
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Usage: solid2fastq.pl <in.title> <out.prefix>
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Note: <in.title> is the string showed in the `# Title:' line of a
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".csfasta" read file. Then <in.title>F3.csfasta is read sequence
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file and <in.title>F3_QV.qual is the quality file. If
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<in.title>R3.csfasta is present, this script assumes reads are
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paired; otherwise reads will be regarded as single-end.
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The read name will be <out.prefix>:panel_x_y/[12] with `1' for R3
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tag and `2' for F3. Usually you may want to use short <out.prefix>
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to save diskspace. Long <out.prefix> also causes troubles to maq.
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};
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getopts('', \%opts);
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die($usage) if (@ARGV != 2);
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my ($title, $pre) = @ARGV;
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my (@fhr, @fhw);
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my @fn_suff = ('F3.csfasta', 'F3_QV.qual', 'R3.csfasta', 'R3_QV.qual');
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my $is_paired = (-f "$title$fn_suff[2]" || -f "$title$fn_suff[2].gz")? 1 : 0;
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if ($is_paired) { # paired end
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for (0 .. 3) {
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my $fn = "$title$fn_suff[$_]";
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$fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz");
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open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n");
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}
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open($fhw[0], "|gzip >$pre.read2.fastq.gz") || die; # this is NOT a typo
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open($fhw[1], "|gzip >$pre.read1.fastq.gz") || die;
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open($fhw[2], "|gzip >$pre.single.fastq.gz") || die;
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my (@df, @dr);
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@df = &read1(1); @dr = &read1(2);
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while (@df && @dr) {
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if ($df[0] eq $dr[0]) { # mate pair
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print {$fhw[0]} $df[1]; print {$fhw[1]} $dr[1];
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@df = &read1(1); @dr = &read1(2);
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} else {
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if ($df[0] le $dr[0]) {
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print {$fhw[2]} $df[1];
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@df = &read1(1);
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} else {
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print {$fhw[2]} $dr[1];
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@dr = &read1(2);
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}
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}
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}
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if (@df) {
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print {$fhw[2]} $df[1];
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while (@df = &read1(1, $fhr[0], $fhr[1])) {
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print {$fhw[2]} $df[1];
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}
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}
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if (@dr) {
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print {$fhw[2]} $dr[1];
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while (@dr = &read1(2, $fhr[2], $fhr[3])) {
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print {$fhw[2]} $dr[1];
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}
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}
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close($fhr[$_]) for (0 .. $#fhr);
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close($fhw[$_]) for (0 .. $#fhw);
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} else { # single end
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for (0 .. 1) {
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my $fn = "$title$fn_suff[$_]";
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$fn = "gzip -dc $fn.gz |" if (!-f $fn && -f "$fn.gz");
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open($fhr[$_], $fn) || die("** Fail to open '$fn'.\n");
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}
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open($fhw[2], "|gzip >$pre.single.fastq.gz") || die;
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my @df;
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while (@df = &read1(1, $fhr[0], $fhr[1])) {
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print {$fhw[2]} $df[1];
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}
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close($fhr[$_]) for (0 .. $#fhr);
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close($fhw[2]);
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}
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sub read1 {
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my $i = shift(@_);
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my $j = ($i-1)<<1;
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my ($key, $seq);
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my ($fhs, $fhq) = ($fhr[$j], $fhr[$j|1]);
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while (<$fhs>) {
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my $t = <$fhq>;
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if (/^>(\d+)_(\d+)_(\d+)_[FR]3/) {
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$key = sprintf("%.4d_%.4d_%.4d", $1, $2, $3); # this line could be improved on 64-bit machines
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die(qq/** unmatched read name: '$_' != '$_'\n/) unless ($_ eq $t);
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my $name = "$pre:$1_$2_$3/$i";
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$_ = substr(<$fhs>, 2);
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tr/0123./ACGTN/;
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my $s = $_;
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$_ = <$fhq>;
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s/-1\b/0/eg;
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s/^(\d+)\s*//;
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s/(\d+)\s*/chr($1+33)/eg;
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$seq = qq/\@$name\n$s+\n$_\n/;
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last;
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}
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}
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return defined($seq)? ($key, $seq) : ();
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}
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