There's a problem in the loop that removes items according to a regex. Whenever an item is removed, the items to the right are shifted over, but $i is still incremented. See: 
  my @arr = qw/ foo foozle bar bar2 foo bar foo /;

  for (my $i=0; $i<@arr; $i++) {
    splice(@arr, $i, 1) if ($arr[$i] =~ /bar/);
  }
  print "$_\n" for (@arr);

  ## output: bar2 is NOT removed

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It will fail to check the next item after each match. It's much simpler (and correct-er) to write: 
  @chroms = grep { ! /[pqxy]/i } @chroms;

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Although, if you're dealing with a huge amount of genetic data, this will be very slow. A quick fix to the existing loop would be the slight change: 
  for (my $i=0; $i<@chroms; $i++) {
    splice(@chroms, $i--, 1) if not $chroms[$i] =~ /[pqxy]/i;
  }                 ####

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This still may not be optimal, but it's in-place so should be faster than the grep.

About your second question... Off the top of my head, I'm not sure what's up with your regex... It's late for me!

blokhead

In reply to Re: regexp and substitute operator problem by blokhead
in thread regexp and substitute operator problem by dannoura

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