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#!/usr/bin/env perl
use strict;
use warnings;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use Fastq_reader;
my $usage = "usage: $0 file.fastq\n\n";
my $fastq_file = $ARGV[0] or die $usage;
main: {
my $fastq_reader = new Fastq_reader($fastq_file);
my $tab_tmp_file = "$fastq_file.tab";
open (my $ofh, ">$tab_tmp_file") or die $!;
while (my $fq_entry = $fastq_reader->next()) {
my $fq_record = $fq_entry->get_fastq_record();
chomp $fq_record;
my @lines = split(/\n/, $fq_record);
print $ofh join("\t", @lines) . "\n";
}
close $ofh;
## sort by read name
my $cmd = "sort -S 4G -T . -k1,1 $tab_tmp_file > $tab_tmp_file.sort";
&process_cmd($cmd);
unlink($tab_tmp_file);
## convert back to fastq file format
$cmd = "cat $tab_tmp_file.sort | sed s/\\\\t/\\\\n/g > $fastq_file.sorted.fq";
&process_cmd($cmd);
unlink("$tab_tmp_file.sort");
exit(0);
}
####
sub process_cmd {
my ($cmd) = @_;
print STDERR "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
return;
}
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