[Biopython-dev] [Biopython] blastdbcmd

[Peter Cock]

Great - let us know on the list if you have any questions.

Peter

On Fri, Feb 22, 2013 at 6:28 PM, Frederico Moraes Ferreira
<ferreirafm at usp.br> wrote:
> Hi Peter,
> Yes, I meant a Biopython Blast application for blastdbcmd.
> Thanks for the link.
> Best,
> Fred
>
> Em 22-02-2013 14:23, Peter Cock escreveu:
>
>> 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
>>
>
> --
> Dr. Frederico Moraes Ferreira
> Universidade de São Paulo
> Faculdade de Medicina
> Instituto do Coração - Imunologia
> Av. Dr. Enéas de Carvalho Aguiar, 44
> 05403-900     São Paulo - SP
> Brasil
>