[Biopython-dev] [Bug 2381] translate and transcribe methods for the Seq object (in Bio.Seq)

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2381


mmokrejs at ribosome.natur.cuni.cz changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
            Summary|translate and transcibe     |translate and transcribe
                   |methods for the Seq object  |methods for the Seq object
                   |(in Bio.Seq)                |(in Bio.Seq)




------- Comment #53 from mmokrejs at ribosome.natur.cuni.cz  2008-11-25 17:18 EST -------
(In reply to comment #27)
> Created an attachment (id=1032)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1032&action=view) [details]
> Patch to Bio/Seq.py to add start codon handling to translation
> 
> Patch adds a new boolean argument to the translate method and function, called
> "init" (rather than my earlier suggestions like "from_start" or "check_start"
> which could be considered misleading).
> 
> Docstring:
> 
>         init - Boolean, defaults to False.  Should translation check the
>                first codon is a valid initiation (start) codon and translate
>                it as methionine (M)?  If False, nothing special is done with
>                the first codon.

What kind of check is it doing? I think it just forces the first letter to be
'M'.

> 
> 
> Example usage of the translate function,
> 
> >>> from Bio.Seq import translate
> >>> translate("TTGAAACCCTAG")
> 'LKP*'
> >>> translate("TTGAAACCCTAG", init=True, to_stop=True)
> 'MKP'
> >>> translate("TTGAAACCCTAG", init=True)
> 'MKP*'
> >>> translate("TTGAAACCCTAG", to_stop=True)
> 'LKP'

I don't like the "init" argument either. I would call it force_initiator_Met
instead. BTW, non-canonical initiator codon is CUG, where did you found UUG?

Sorry, I got overloaded by many other tasks so haven't read any other
follow-ups, I just hit the email from bugzilla by luck.


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