Hello,

I have a question on perl coding to create a subset of a fastq file. I most take every 40th seqence from a larger file. The oringinal file is so big I cant use arrays and such.

I have this code

use strict;
use warnings;

open (my $fh,"fast.fastq") or die "Failed to open file: $!\n";
open (my $out_fh, "> out10.fastq");
while(<$fh>) {
      chomp;
#$. holds the number of the last read line
#every 40 seq
 next if $. <= 40;

   my $header_line = $_;
   my $seq = <$fh>;
   my $plus = <$fh>;
   my $qualities = <$fh>;
   print $out_fh "$header_line$seq$plus$qualities";

}
close $fh;
close $out_fh;

it skips the first 40 lines which isn't much good to me. And then prints out the rest of the file which also isn't much good to me.

I am looking for a way to loop it so I get every 40th seq not line and all the ways through the file to get the subset.

Thanks