[Biopython] Reading from binary BLAST db

[David Shin]

Hi Peter,

If I understand Alexey's question right, I did have the same problem
before. I wrote a bunch of scripts to work around the problem, but it
appears you have something more straight forward. Can you elaborate?

Thanks,

Dave

On Wed, Mar 4, 2015 at 1:18 AM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> On Wed, Mar 4, 2015 at 6:12 AM, Alexey Morozov
> <alexeymorozov1991 at gmail.com> wrote:
> > Is there any support for compiled BLAST databases (*.pin/*.phr/*.psq)
> I/O in
> > biopython? I need to get complete sequences that match, not just hsps
> that
> > Bio.Blast.NCBIXML can read.
>
> No, but you can call the NCBI BLAST+ tool blastdbcmd to do this
> (or fastacmd from legacy NCBI BLAST).
>
> Peter
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython
>



-- 
David Shin, Ph.D
Lawrence Berkeley National Labs
1 Cyclotron Road
MS 83-R0101
Berkeley, CA 94720
USA
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20150304/7d0e5b7c/attachment.html>