in reply to BioPerl translate sequence

However, when trying to pass options to the sequence object (like -frame => 1 or -complete => 1), the option is introduced into the object: How do I correctly pass an option? Any help is greatly appreciated!

What documentation are you referencing? See http://doc.bioperl.org/releases/bioperl-1.4/Bio/Perl.html#POD8 
 Title   : translate
 Usage   : $seqobj = translate($seq_or_string_scalar)

 Function: translates a DNA sequence object OR just a plain
           string of DNA to amino acids
 Returns : A Bio::Seq object

 Args    : Either a sequence object or a string of
           just DNA sequence characters
So Bio::Seq->translate doesn't expect any kind of complete option

I am trying to translate a DNA sequence to a protein sequence using all 3 ORFs (same strand).

What? ORF sounds like something Pinky would say :D

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Re^2: BioPerl translate sequence
by RobertCraven (Sexton) on May 13, 2011 at 14:07 UTC
    Thank you for your answer. The idea is coming from here:

    BioPerl Wiki

    Gosh, have not seen Pinky in ages... :-D
    Not sure if he would have ever talked about ORFs ;)

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