[BioPython] Problem to obtain Hit length parsing with NCBIXML
Michiel De Hoon
mdehoon at c2b2.columbia.edu
Wed Aug 15 00:45:26 UTC 2007
This should work:
>>> for alignment in brecord.alignments:
... print alignment.length
If it doesn't, please send us the exact code you are using, and the exact
error message that you got.
--Michiel.
Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032
-----Original Message-----
From: biopython-bounces at lists.open-bio.org on behalf of Gabino Sanchez-Perez
Sent: Tue 8/14/2007 7:57 PM
To: biopython at lists.open-bio.org
Subject: [BioPython] Problem to obtain Hit length parsing with NCBIXML
Hi
I'm parsing a blastp output in XML format using NCBIXML, but my problem is
that
I don't know how to get the Hit length (not alignment length), even though is
defined in the parser:
def _end_Hit_len(self):
self._hit.length = int(self._value)
So in my script when I iterate
for alignment in brecord.alignments:
for hsp in alignment.hits:
it seems that is not defined and the error message is that hit.length does
not
exist.
Thanks in advance
Gabino
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