[Biopython-dev] [Bug 2783] Using alternative start codons in Bio.Seq translate method/function

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2783





------- Comment #3 from eric.talevich at gmail.com  2009-03-06 14:54 EST -------
(In reply to comment #2)

How about require_start? Or require_met, if you don't mind how strange it looks
as English. The name with_start_codon seems like it would take a codon or
alternate table as the argument.

I also see two choices being made by using this parameter:
(1) Check that the sequence starts with a valid start codon, and if not, raise
an exception;
(2) Use a set of alternate genetic codes for looking up the initial methionine.

>From the other bug's discussion it seems like there are a number of boolean
options that could reasonably be used with the translate() method, but adding
them all as keyword args would clutter up the API. What about using a bitmask
in Bio.Seq that can be used with translate()? The re module takes a bitmask as
the last parameter for most functions, for example, and it looks pretty clean
compared to a series of boolean keyword args.


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