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#!/usr/bin/perl -w
##
# fastq_to_tabbed.pl
#
# Convert a pair of FASTQ files to a single file in a one-pair-per-line
# format, where each line has these five tab-delimited fields:
#
# 1. Pair name
# 2. Sequence of mate 1
# 3. Qualities of mate 1
# 4. Sequence of mate 2
# 5. Qualities of mate 2
#
# This script comes in handy if (a) you'd just like to store your
# paired-end data in a less awkward format than the usual pair of
# parallel FASTQ files, or (b) you'd like to use Bowtie with gzipped
# paired-end input without unzipping it first. In that case, you can
# pipe the output of this script (which handles gzipped inputs by
# piping them through gzip -dc) to Bowtie and use '--12 -'.
#
# Note that this script can also handle unpaired input (with -u), which
# Bowtie handles approrpaitely in --12 mode even when it's intermingled
# with paired-end input.
#
use strict;
use warnings;
use Getopt::Long;
# Courtesy: http://www.perlmonks.org/?node_id=625977
sub shuffle (@) {
my @a = \(@_);
my $n;
my $i = @_;
map {
$n = rand($i--);
(${$a[$n]}, $a[$n] = $a[$i])[0];
} @_;
}
my $unpaired = "";
my $mate1 = "";
my $mate2 = "";
my $shuffle = 0;
GetOptions ("u=s" => \$unpaired,
"1=s" => \$mate1,
"2=s" => \$mate2,
"shuffle" => \$shuffle) || die "Bad option";
my @output;
my @unpaireds = split(/,/, $unpaired);
for my $f (@unpaireds) {
open UNP, "$f" || die;
while(<UNP>) {
chomp;
my $name = $_;
$name = substr($name, 1);
my $seq = <UNP>;
chomp($seq);
my $name2 = <UNP>;
my $qual = <UNP>;
chomp($qual);
push @output, "$name\t$seq\t$qual\n";
}
close(UNP);
}
my @mate1s = split(/,/, $mate1);
my @mate2s = split(/,/, $mate2);
for(my $i = 0; $i <= $#mate1s; $i++) {
if($mate1s[$i] =~ /\.gz$/) {
open M1, "gzip -dc $mate1s[$i] |" || die;
} else {
open M1, "$mate1s[$i]" || die;
}
if($mate2s[$i] =~ /\.gz$/) {
open M2, "gzip -dc $mate2s[$i] |" || die;
} else {
open M2, "$mate2s[$i]" || die;
}
while(<M1>) {
my $name1 = $_;
chomp($name1);
$name1 = substr($name1, 1, -2);
my $name2 = <M2>;
chomp($name2);
$name2 = substr($name2, 1);
my $seq1 = <M1>;
chomp($seq1);
my $seq2 = <M2>;
chomp($seq2);
my $tmp = <M1>;
$tmp = <M2>;
my $qual1 = <M1>;
chomp($qual1);
my $qual2 = <M2>;
chomp($qual2);
print "$name1\t$seq1\t$qual1\t$seq2\t$qual2\n" unless $shuffle;
push @output, "$name1\t$seq1\t$qual1\t$seq2\t$qual2\n" if $shuffle;
}
close(M1);
close(M2);
}
if($shuffle) {
@output = shuffle(@output);
print join("", @output);
}
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