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#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use lib("/usr/lib/trinityrnaseq/PerlLib");
use Fastq_reader;
use Data::Dumper;
my $help_flag;
my $usage = <<__EOUSAGE__;
#############################################################################################
#
# --samples_file <string> samples.txt
#
# --output_prefix <string> outputs will be named <string>.left.fq and <string>.right.fq
#
#############################################################################################
__EOUSAGE__
;
my $samples_file;
my $output_prefix;
&GetOptions ( 'h' => \$help_flag,
'samples_file=s' => \$samples_file,
'output_prefix=s' => \$output_prefix,
);
unless ($samples_file && $output_prefix) {
die $usage;
}
main: {
my @samples = &parse_samples_file($samples_file);
# init fq readers
foreach my $sample (@samples) {
my $left_fq = $sample->{left_fq};
my $left_fq_reader = new Fastq_reader($left_fq);
$sample->{left_fq_reader} = $left_fq_reader;
my $right_fq = $sample->{right_fq};
my $right_fq_reader = new Fastq_reader($right_fq);
$sample->{right_fq_reader} = $right_fq_reader;
}
# open output files:
my $left_fq_outfile = "$output_prefix.left.fq";
open(my $left_ofh, ">$left_fq_outfile") or die "Error, cannot write to $left_fq_outfile";
my $right_fq_outfile = "$output_prefix.right.fq";
open(my $right_ofh, ">$right_fq_outfile") or die "Error, cannot write to $right_fq_outfile";
my $samples_remaining = scalar(@samples);
my $counter = 0;
while($samples_remaining != 0) {
$samples_remaining = 0;
foreach my $sample (@samples) {
if ($sample->{done}) { next; }
my $sample_name = $sample->{sample_name};
my $left_fq_reader = $sample->{left_fq_reader};
my $left_fq_entry = $left_fq_reader->next();
my $right_fq_reader = $sample->{right_fq_reader};
my $right_fq_entry = $right_fq_reader->next();
if ($left_fq_entry xor $right_fq_entry) {
confess "Error, found left_fq entry but not right_fq entry: " . Dumper([$sample, $left_fq_entry, $right_fq_entry]);
}
elsif ($left_fq_entry && $right_fq_entry) {
print $left_ofh $left_fq_entry->get_fastq_record();
print $right_ofh $right_fq_entry->get_fastq_record();
$samples_remaining = 1;
$counter++;
if ($counter % 100000 == 0) {
print STDERR "\r[$counter] ";
}
}
else {
$sample->{done} = 1;
$sample->{left_fq_reader}->finish();
$sample->{right_fq_reader}->finish();
}
}
} # end of while samples remaining
close $left_ofh;
close $right_ofh;
print STDERR "\n\nDone. Output $counter fastq records per file.\n";
exit(0);
}
####
sub parse_samples_file {
my ($samples_file) = @_;
my @samples;
open(my $fh, $samples_file) or die "Error, cannot open file: $samples_file";
while(<$fh>) {
chomp;
my ($sample_name, $left_fq, $right_fq) = split(/\t/);
push (@samples, { sample_name => $sample_name,
left_fq => $left_fq,
right_fq => $right_fq,
} );
}
close $fh;
return(@samples);
}
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