[Biopython] Reading from binary BLAST db

[Alexey Morozov]

David, could you please mail me said scripts? I'm gonna make a reader
library, perhaps SeqIO-compatible and it'll be great if I can reuse your
code. I think mailing list doesn't support file attachments, so please use
my e-mail or some file hosting.
Blastdbcmd is a nice thing, and may indeed need a wrapper, but I can easily
imagine a situation when one has a DB, but doesn't have blastdbcmd (I'm in
such a situation myself, actually, and installing software to the cluster
we use may be a hassle). So I'd rather have a code with as little
dependencies as possible.

2015-03-04 18:22 GMT+08:00 Peter Cock <p.j.a.cock at googlemail.com>:

> Hi David,
>
> If you run a BLAST search you can get the ID of a matched sequence
> (and the matching region of the sequence). Using blastdbcmd you
> can get the entire matching sequence from the BLAST DB using
> their ID (or ask for multiple sequences by giving several IDs). The
> sequences can be output in FASTA format.
>
> Note Bio.Blast.Applications doesn't yet have a wrapper to help
> calling blastdbcmd from within Python - that would be a nice addition.
>
> Peter
>
> On Wed, Mar 4, 2015 at 9:59 AM, David Shin <davidsshin at lbl.gov> wrote:
> > 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
>



-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.
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