[BioPython] parsing the blastoutput and printing the alingment
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
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:
Latest code is available here:
It also gets rid of this annoying message:
UserWarning: qblast works only with blastn and blastp for now.
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