#! perl -sw use strict; my %outFHs = map { open my $fh, '>', "$_.fastQ" or die $!; $_ => $fh; } qw[ TTGT GGTT ACCT other ]; until( eof() ) { my @lines = map scalar <>, 1 .. 4; my $barcode = substr $lines[1], 0, 9; my $tag = substr $barcode, 3, 4; print { $outFHs{ $tag } // $outFGs{ other } } @lines; } __END__ usage: thisScript theBigfile.fastQ ## outputs to TTGT.fastQ GGTT.fastQ ACCT.fastQ ## Unrecognised records are put into "other.fastQ"