[BioPython] Translation method for Seq object

[Michiel de Hoon]

(f) Use .translate both for the Python .translate and for the Biopython .translate.

S.translate() ===> Biopython .translate

S.translate(table [,deletechars]) ===> Python .translate

We can tell from the presence or absence of arguments whether the user intends Python's translate or Biopython's translate.

--Michiel.



--- On Mon, 10/13/08, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: [BioPython] Translation method for Seq object
> To: "BioPython Mailing List" <biopython at lists.open-bio.org>
> Date: Monday, October 13, 2008, 8:38 AM
> Dear Biopythoneers,
> 
> This is a request for feedback about proposed additions to
> the Seq
> object for the next release of Biopython.  I'd like
> people to pick (a)
> to (e) in the list below (with additional comments or
> counter
> suggestions welcome).
> 
> Enhancement bug 2381 is about adding transcription and
> translation
> methods to the Seq object, allowing an object orientated
> style of
> programming.
> 
> e.g. Current functional programming style:
> 
> >>> from Bio.Seq import Seq, transcribe
> >>> from Bio.Alphabet import generic_dna
> >>> my_seq = Seq("CAGTGACGTTAGTCCG",
> generic_dna)
> >>> my_seq
> Seq('CAGTGACGTTAGTCCG', DNAAlphabet())
> >>> transcribe(my_seq)
> Seq('CAGUGACGUUAGUCCG', RNAAlphabet())
> 
> With the latest Biopython in CVS, you can now invoke a Seq
> object
> method instead for transcription (or back transcription):
> 
> >>> my_seq.transcribe()
> Seq('CAGUGACGUUAGUCCG', RNAAlphabet())
> 
> For a comparison, compare the shift from python string
> functions to
> string methods.  This also makes the functionality more
> discoverable
> via dir(my_seq).
> 
> Adding Seq object methods "transcribe" and
> "back_transcribe" doesn't
> cause any confusion with the python string methods. 
> However, for
> translation, the python string has an existing
> "translate" method:
> 
> > S.translate(table [,deletechars]) -> string
> >
> > Return a copy of the string S, where all characters
> occurring
> > in the optional argument deletechars are removed, and
> the
> > remaining characters have been mapped through the
> given
> > translation table, which must be a string of length
> 256.
> 
> I don't think this functionality is really of direct
> use for sequences, and
> having a Seq object "translate" method do a
> biological translation into
> a protein sequence is much more intuitive. However, this
> could cause
> confusion if the Seq object is passed to non-Biopython code
> which
> expects a string like translate method.
> 
> To avoid this naming clash, a different method name would
> needed.
> 
> This is where some user feedback would be very welcome - I
> think
> the following cover all the alternatives of what to call a
> biological
> translation function (nucleotide to protein):
> 
> (a) Just use translate (ignore the existing string method)
> (b) Use translate_ (trailing underscore, see PEP8)
> (c) Use translation (a noun rather than verb; different
> style).
> (d) Use something else (e.g. bio_translate or ...)
> (e) Don't add a biological translation method at all
> because ...
> 
> Thanks,
> 
> Peter
> 
> See also http://bugzilla.open-bio.org/show_bug.cgi?id=2381
> _______________________________________________
> BioPython mailing list  -  BioPython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython