Question: Biopython Ncbixml: Retrieve Used Word_Size
gravatar for Marc
7.5 years ago by
Marc0 wrote:

I know I can retrieve the expect value, window_size etc that was used submitting the query from the Blast recordclass, but I don't seem to find the wordsize as well. Is there any way to retrieve the set wordsize from the xml file?

biopython blast • 1.2k views
ADD COMMENTlink written 7.5 years ago by Marc0
gravatar for Leszek
7.5 years ago by
IIMCB, Poland
Leszek4.0k wrote:

I found Word size object neither in Biopython NBCIXML class specification, nor in XML blast results, nor in blast txt results.

You should know the word size from you query. If you didn't change the default value, I think it's 3 for blastp and 11 for blastn.

ADD COMMENTlink written 7.5 years ago by Leszek4.0k

Thanks. Strange that blast logs the settings for expect, but not for word_size. I don't always know the settings, as these blast-actions are usually performed by other people. So I guess I have to log their settings somewhere when they submit their query.

ADD REPLYlink written 7.5 years ago by Marc0
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