[BioPython] blast output xml

[Michiel De Hoon]

Hi Javier,

> I followed the tutorial cookbook steps but I got the same exception (see
> below). The output I got running blast locally is not XML but text. I guess
> it might be related to the version I'm using (python 2.5, biopython
> 1.42.2on ubuntu 7.4). Any idea?

Use Biopython 1.43.

> On the other hand I think there is a mistake in the cookbook, instead of:
> >>> from Bio.Blast import NCBIXML
> >>> blast_records = NCBIXML.parse(result_handle)
> I think it should be:
> >>> blast_parser= NCBIXML.BlastParser()
> >>> blast_result=blast_parser.parse(result_handle)

The description in the cookbook is correct for Biopython 1.43.

As a note to the developers:
We should ask ourselves if distributing packages for various linuxes is
really a good idea. Installing Biopython isn't all that hard, and the
packages for linux tend to get behind as new Biopython versions come out,
causing confusion for our users.

--Michiel.


Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1150 St Nicholas Avenue
New York, NY 10032