[BioPython] HELP!

[Peter]

On Wed, Apr 1, 2009 at 4:56 AM, Hermella Woldemdihin <hermifi at yahoo.com> wrote:
> Hi everyone,
> I am trying to write a bio-python script that uses SwissProt accession
> numbers to download a sequence objects and then run remote blast
> with the sequences. Then download good hit sequences listed in Blast
> results and print their sequences.I am using a Windows based system
> with bio-python 2.5, if someone could help me out I would really
> appreciate it with some sample code or something. I just started
> learning python and have tried to follow the documentation and
> cookbook without much success, my programming experience is
> virtually non-existent. Thanks.
> Hermi

Hello Hermi and Abdi Worku Muleta,

You've both emailed almost identical questions at almost the same time
- are you doing the same project for a university assignment?

First of all, the Biopython Tutorial and Cookbook doesn't try to teach
you python - it assumes you at least know the basics.  Have a look at
www.python.org for some beginners guides, or check you library as
there are plenty of books for learning Python.

To download SwissProt functions, look at the Bio.ExPASy.get_sprot_raw
function from Bio.ExPASy (there is an example in the Tutorial, search
for get_sprot_raw).  You can also use Bio.Entrez.eftech, but I have
found the NCBI only seem to keep track of the latest SwissProt
identifiers, so using ExPASy should be more reliable.

If you want to run BLAST on these records, then can do this for one
query sequence at a time using Bio.Blast.NCBIWWW.qblast (again there
is an example in the Tutorial, search for qblast).  You could also
install standalone BLAST from the NCBI on your own machine and do all
the query sequences together in a FASTA file, but I think this might
be a bit complicated for a novice.

Peter