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bin/bp_genbank_ref_extractor  view on Meta::CPAN

  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]) {
    if    (/embl/i)       {return '.embl';}
    elsif (/entrezgene/i) {return '.asn';}
    elsif (/fasta/i)      {return '.fasta';} # fasta|fast|fas|seq|fa|fsa|nt|aa|fna|faa
    elsif (/fastq/i)      {return '.fastq';}
    elsif (/gcg/i)        {return '.gcg';}
    elsif (/genbank/i)    {return '.gb';} # gb|gbank|genbank|gbk|gbs
    elsif (/swiss/i)      {return '.swiss';} # swiss|sp
    else {
      log_it (9, "DEBUG: couldn't find the right extension for the requested format. Using '.seq' as default.");