[BioPython] parsing the blastoutput and printing the alingment
Muthuraman, Manickam
manickam.muthuraman at wur.nl
Fri Jun 16 08:42:08 UTC 2006
Thanks peter
After overwriting the NCBIWWW.py header file my script works.
once again i would like to thank
from
manickam
-----Original Message-----
From: Peter [mailto:biopython at maubp.freeserve.co.uk]
Sent: Fri 6/16/2006 12:31 AM
To: Muthuraman, Manickam
Cc: biopython at lists.open-bio.org
Subject: Re: [BioPython] parsing the blastoutput and printing the alingment
Muthuraman, Manickam wrote:
> Dear Peter
>
> In this mail i am attaching three files :seq file,python script file
> and the blast output. I am using python Python 2.4.1 (#2, Aug 25
> 2005, 18:20:57)and biopython 1.40
Your attachment came as a weird winmail.dat file - something Outlook
and the Microsoft Exchange Client sometimes does. There is a Linux tool
to "unzip" the file called tnef, which I installed on Ubuntu with a
simple "apt-get install tnef"
Anyway, the problem is simply that your XML file has this little HTTP
header at the start:
HTTP/1.1 200 OK
Date: Thu, 15 Jun 2006 21:23:08 GMT
Server: Nde
Content-Type: application/xml
Connection: close
If you edit the file to remove this, the BioPython can read the file fine.
Looking over my old email, Michiel de Hoon checked in a fix from
Alexander Morgan for this in March. You need to update this file:
/usr/lib/python2.4/site-packages/Bio/Blast/NCBIWWW.py
Latest code is available here:
http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Blast/NCBIWWW.py?cvsroot=biopython
It also gets rid of this annoying message:
UserWarning: qblast works only with blastn and blastp for now.
Peter
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