[Biopython] NCBIWWW and megablast

Bart bratdaking at gmail.com
Fri Oct 8 12:00:53 UTC 2010


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



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