[BioPython] qblast fails on parsing XML results
Ilya Soifer
ilya.soifer at gmail.com
Mon Feb 27 10:38:39 EST 2006
Hi,
I hope that I send it to the correct list.
When I run qblast I get
>>> res1 = NCBIWWW.qblast("blastn", "nr", seq1)
Traceback (most recent call last):
File "<pyshell#24>", line 1, in -toplevel-
res1 = NCBIWWW.qblast("blastn", "nr", seq1)
File "C:\Python24\Lib\site-packages\Bio\Blast\NCBIWWW.py", line
1130, in qblast
i = results.index("Connection: close")
ValueError: substring not found
This happens since the results that Blast return no longer have this header
# HTTP/1.1 200 OK
# Date: Wed, 05 Oct 2005 02:13:33 GMT
# Server: Nde
# Content-Type: text/plain
# Connection: close
#
but this one
HTTP/1.0 200 OK
Date: Mon, 27 Feb 2006 11:54:40 GMT
Content-Type: application/xml
Server: Nde
Via: 1.1 proxy7 (NetCache NetApp/6.0.2)
I guess it might be better to look for something like "<?xml" etc. in
order to remove the annoying header.
Ilya
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