[Biopython] NCBIWWW and megablast

[Peter]

On Fri, Oct 8, 2010 at 1:00 PM, Bart <bratdaking at gmail.com> wrote:
> Hey,
>
> I was wondering why the megablast option (the greedy extension) in the
> qblast is left out in the NCBIWWW.py?
> I want to map a sequence to the human genome, and to mimic the NCBI website
> I need a gapcost setting of "0 0", with the megablast option set to True.
> The fix was to add the following line
>       ('LCASE_MASK',lcase_mask),
>       ('MEGABLAST',megablast),
>       ('MATRIX_NAME',matrix_name),
> to the parameters list of the qblast def and add:
> megablast=None,
> to the arguments.
> But is there a reason this setting has been left out (it is as far as I can
> see the only setting from the NCBI api missing)?
>
> Cheers,
> Bart

Hi Bart,

Most likely this is a relatively recent addition to the NCBI API.
Could you turn that into a patch we could apply? Don't forget to add
the new option to the qblast function's docstring.

Thanks,

Peter