Hi heavenfeel,

The following is a demonstration using the MCE::Loop module. What is nice about MCE is the ability to process a file containing multiple records. The record separator for a fastq file is "\n@" which anchors @ at the start of the line. MCE detects "\n" at the start of the record separator.

MCE is a chunking engine allowing a worker to receive several records at a time. The effect is a reduction in the number of trips to and from the MCE-manager process.

The logic below allows one to search multiple patterns. Simply change the patterns to suite your needs. Perhaps, this can read patterns stored in a file. Anyway, this is a small MCE demonstration. The MCE->print statement prints the entire record to STDOUT.

use strict;
use warnings;

use MCE::Loop;

my @patterns = ( "biopattern1", "biopattern2", "biopattern3" );
my $search   = join('|', @patterns);
my $regex    = qr/$search/;

open my $fh, "gunzip -c in.fastq.gz |" or die "open error: $!";

MCE::Loop->init(
    max_workers => 4,
    chunk_size => 50,
    RS => "\n@"
);

MCE::Loop->run( sub {
    my ( $mce, $chunk_ref, $chunk_id ) = @_;

    for my $i ( 0 .. $#{ $chunk_ref } ) {
        if ( $chunk_ref->[$i] =~ /$regex/ ) {
            MCE->print( $chunk_ref->[$i] );
        }
    }

}, $fh );

MCE::Loop->finish();

close $fh;
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