[Biopython-dev] Adjusting the xxMotif wrapper / Bio.Application plans

Christian Brueffer christian at brueffer.de
Thu Aug 8 10:37:19 UTC 2013

On 8/7/13 0:51 , Peter Cock wrote:
> Hi Christian et al.,
> I've just noticed something in the XXmotif wrapper which
> I should have raised back in November 2012 when it was
> committed. This is to do with the way the options were
> define, e.g.
>       _Option(["--negSet", "negSet", "negset", "NEGSET"],
>                    "sequence set which has to be used as a reference set",
>                    filename = True,
>                    equate = False),
> The first argument is a list of names, aliases which can
> be used via the (legacy) set_parameter method. Of
> these the first is what goes in the actual command
> string, and the last must be a valid Python identifier
> and becomes a property and a keyword argument
> for the __init__ method (and ideally follow PEP8
> guidelines).

Yeah, unfortunately I wasn't aware of this detail.

> Normally the _Option would just have TWO alias,
> in this case ["--negSeq, "negset"] would seem best.
> Clearly I'd not documented this well enough, but
> I've tried to make this more explicit now:
> https://github.com/biopython/biopython/commit/39a88714ab7ee7a8dc4ed2b7a7ea71569fdd4293
> Was there a special reason for all these case variants
> in the XXmotif options??

I basically followed the example set by
Bio/Align/Applications/_Clustalw.py.  The "rationale" was to allow for
people to use their
favourite spelling variety.

I guess it was bad luck this happened to serve as an example, as it
was the first piece of code I ever touched in BioPython.

It would be nice to streamline all application wrappers in this regard


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