Here's an option that uses Tie::File to bind the fastq records' file to an array for processing. The files will automatically close when my %FHs falls out of scope. My thanks to BrowserUk for the elegant file handle/hash routine.

use Modern::Perl;
use Tie::File;

{
    tie my @fastqLines, 'Tie::File', 'records.fastq', recsep => "\n" o
+r die $!;

    my %FHs = map {
        open my $fh, '>', "$_.fastq" or die $!;
        $_ => $fh
    } qw[ TTGT GGTT ACCT ];

    for ( my $i = 0 ; $i < scalar @fastqLines ; $i += 4 ) {
        $fastqLines[ $i + 1 ] =~ /^...(.{4})/
          and print { $FHs{$1} } @fastqLines[ $i .. $i + 3 ];
    }

    untie @fastqLines;
}

[download]

Update: Don't try this at home, as the OP's 34G file is much too large for Tie::File to efficiently handle.

In reply to Re: Deconvolutinng FastQ files by Kenosis
in thread Deconvolutinng FastQ files by snakebites

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