[BioPython] Translation method for Seq object

[Leighton Pritchard]

On 19/10/2008 19:52, "Peter" <biopython at maubp.freeserve.co.uk> wrote:

> I'm still a tiny bit uneasy about the name clash myself... anyone else
> what to join in the debate?

The problem domain for biological sequences implies a natural definition for
the application of 'translate' to a DNA/RNA sequence that is the translation
into protein sequence.  The string.translate() method is not consistent with
this natural use of the language of the problem domain.

I take Martin's point that there are valid uses for the string.translate()
method in bioinformatics and elsewhere, but I think that overloading
translate() is as valid here as overloading __mul__ would be for an
implementation of matrix algebra, or complex numbers.  For biological
sequences as much as for number types, I think the problem domain and
expected behaviour of the object being represented in code should take
precedence over emulation of an object type that was never intended to
provide the functionality required for a biological sequence.

I think also that if the string.translate() method is required, an explicit
call to string.translate() implies: "translate this biological sequence as
if it were a string, and not a biological sequence".  The converse
application of a Bio.translate() method would to me imply "translate this
biological sequence as if it were a biological sequence, and not a string";
which seems to me to defeat part of the purpose of representing the
biological sequence with its own object.

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405


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