[Biopython] remote blast against SRA database with biopython

[assaf www]

Christopher, I was not aware of eutils einfo, I assume you mean the following?
http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EInfo
I will look into it.
Peter, I wouldn't mind contributing functions when I figure out what
should be done here, though my knowledge/experience of how to look at
biopython from the developer side is zero, so i may mainly cause
damage :)

Assaf

On Sun, Dec 21, 2014 at 7:54 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> Does the SRA blast database  show up in eutils einfo?
>
> Chris
>
>
> -------- Original message --------
> From: Peter Cock
> Date:12/21/2014 8:47 AM (GMT-06:00)
> To: assaf www
> Cc: Biopython Mailing List
> Subject: Re: [Biopython] remote blast against SRA database with biopython
>
> I was hoping it could be done with BLAST+ and the -remote option,
> but that doesn't seem to work - maybe I have guessing the SRA
> database name wrong?
>
> $ blastn -query example -db sra -max_target_seqs 3 -outfmt 6 -remote
> Warning: Error initializing remote BLAST database data loader:
> Nucleotide BLAST database 'sra' does not exist in the NCBI servers
> BLAST Database error: 'sra' not found on NCBI servers.
>
> And:
>
> $ blastn -query example.fasta -db SRA -max_target_seqs 3 -outfmt 6 -remote
> Warning: Error initializing remote BLAST database data loader:
> Nucleotide BLAST database 'SRA' does not exist in the NCBI servers
> BLAST Database error: 'SRA' not found on NCBI servers.
>
> In terms of the Biopython QBLAST function, that now uses
> http://blast.ncbi.nlm.nih.gov/Blast.cgi internally, but does not
> set the BLAST_SPEC parameter which is not officially in the
> docmentation: http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html
>
> Either that documentation is out of date, or using this would
> be unofficial... but you could try extending that function?
>
> Regards,
>
> Peter
>
>
> On Sun, Dec 21, 2014 at 11:09 AM, assaf www <assafwww at gmail.com> wrote:
>> hi there,
>> I would like to use remote blast against SRA database
>> (http://www.ncbi.nlm.nih.gov/sra) with biopython, for specific
>> experiments
>>
>> on the NCBI blast it is done from:
>>
>> https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=SRA&DB_GROUP=Exp
>>
>> do you maybe have and idea whether this can be done with biopython ?
>> for example with NCBIWWW.qblast() or otherwise ?
>>
>> thanks a lot
>> Assaf
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