[Biopython] Reading from binary BLAST db

[Peter Cock]

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
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>
>
>
>
> --
> David Shin, Ph.D
> Lawrence Berkeley National Labs
> 1 Cyclotron Road
> MS 83-R0101
> Berkeley, CA 94720
> USA