[BioPython] plain txt blast output - xml instead

Peter biopython at maubp.freeserve.co.uk
Wed Jun 14 17:54:53 EDT 2006


Rohini Damle wrote:
> Thank you very much for your help.
> I have 55-56 proteins & I am using Blast to find out short, nearly exact
> matches. The xml parser works fine for first record but even if I used the
> iterator, I CAN NOT ITERATE through the records, I have used the same code
> as u have given, what might be wrong?
> Rohini.

If you you send us a short be of example code, and the error message 
that would help.  Also, what version of BioPython are you using, and do 
you have Windows or Linux or MacOS...

One guess is that you will need to update the NCBIStandalone.py file to 
include a recent fix for iterating XML files.

Assuming you are using BioPython 1.41 on Windows, the click on this link 
and pick "download" near the top of the page to get the latest verion:

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/Blast/NCBIStandalone.py?cvsroot=biopython

Save it here:

c:\python24\lib\site-packages\Bio\Blast\NCBIStandalone.py

(Make a copy of the old file first, just in case)

Peter



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