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  if (!@_ || $_[0] eq 'here') {
    $level = 1;
  } elsif ($_[0] eq 'before'){
    $level = 2;
  } elsif ($_[0] =~ /^[0-9]+$/){
    $level = 1 + $_[0];
  } else {
    die "Bug found when calculating level for caller function. Please report.";
  }
  my $deeper = shift;
  return "by " . (caller($level))[3] . " at line " . (caller($level))[2];
}


sub file_extension_for {
  ## TODO in some cases, extension changes whether it's protein or DNA or whatever
  ## and this should be supported
  ## XXX there must be a more elegant to handle the formats on this scripts

  ## to update this list, look in the _guess_format method, inside SeqIO.pm of bioperl
  for ($_[0]) {