[BioPython] parsing the blastoutput and printing the alingment

Peter biopython at maubp.freeserve.co.uk
Thu Jun 15 18:31:59 EDT 2006


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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