[Biopython] multiple sequence blast

[Peter Cock]

On Thu, Jun 30, 2011 at 11:42 AM, Brad Chapman <chapmanb at 50mail.com> wrote:
> Dilara;
> Thanks for the message. It would be helpful if you'd include the
> error message traceback that you got stuck on; this will help
> pinpoint the problem.
>
> From reading your code, my guess is that you are getting and IOError
> about files not existing. When you do os.listdir, it only includes
> the name of the files, not the full path to where they are located.

I would have suggested the same thing.

In addition, are you really trying to run 100,000 contigs though
the NCBI online BLAST service? If it works it will take a long time,
but they might not like that and block your access. Big BLAST
jobs like this are better done by installing BLAST+ (and in this case
the NR database) locally. Biopython has wrappers to help call
standalone BLAST too.

Peter