[Biopython] (no subject)
Stefanie Lück
lueck at ipk-gatersleben.de
Wed May 27 07:06:34 UTC 2009
Hi David!
I found the problem. I got allways the same start for the hsp.query_start
and was wonder whats happened. I had a mistake in my code. Sorry for your
waste of time!
S.
----- Original Message -----
From: "David Winter" <winda002 at student.otago.ac.nz>
To: <biopython at biopython.org>
Sent: Wednesday, May 27, 2009 3:18 AM
Subject: [Biopython] (no subject)
Stefanie Lück wrote:
> Hi!
>
> Is there a way to get the query start information of the hit in the
xml output?
> Alternatively I can find the hit on the query
Hi Stefanie,
The query_start is in the "hsp" instance for each alignment in each
blast record, if you have a record called b_record you can do this:
>>>for alignment in b_record.alignments:
>>> for hsp in alignment.hsps:
>>> print "hit '%s' matches query '%s' starting a query position
%i" % (alignment.title, b_record.query, hsp.query_start )
hit 'gene1' matches query 'my_query1' from query position 841
hit 'gene2' matches query 'my_query1' from query position 190
There is a nice diagram of all the 'stuff' in the blast record class in
the tutorial here:
http://www.biopython.org/DIST/docs/tutorial/Tutorial.html#fig:blastrecord
Hope that helps you do what you want to,
David
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