[Biopython] blastdbcmd

[Peter Cock]

On Fri, Feb 22, 2013 at 5:01 PM, Frederico Moraes Ferreira
<ferreirafm at usp.br> wrote:
> Hi there Biopythoneers,
> As long as I know, there isnt't a blastdbcmd submodule into Biopython. So,
> I've been writing the blast matched sequences ID's to a file, fetching them
> all with a subprocess and reading with SeqIO afterwards. In some cases,
> however, I miss a blastdbcmd parser to make things easy. How do you guys are
> dealing with this?
> Best,
> Fred

Are you talking about a command line wrapper for blastdbcmd, to go in
Bio/Blast/Applications.py? That seems a good idea.

Personally I find the blastdbcmd tool quite handicapped due to the
introduction of generated sequence identifiers, and rarely use it:
http://blastedbio.blogspot.co.uk/2012/10/my-ids-not-good-enough-for-ncbi-blast.html

Instead I would use Bio.SeqIO to index the FASTA file used for the
database, and get the sequences that way.

Peter