[Biopython] remote blast against SRA database with biopython
Fields, Christopher J
cjfields at illinois.edu
Sun Dec 21 23:49:47 UTC 2014
Sorry, replied in transit. Eutils einfo/esummary I think can be used to get blast database information for URL API settings. I believe the eutils DB is 'blastdb'.
Chris
Sent from my iPad
> On Dec 21, 2014, at 3:55 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
>> On Sun, Dec 21, 2014 at 9:10 PM, assaf www <assafwww at gmail.com> wrote:
>> 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.
>
> Biopython has Bio.Entrez for accessing this in Python code.
>
>> 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
>
> This may not be the easiest task to attempt - but have a go,
> you're not going to break things for anyone else (even if
> you do have to reinstall Biopython on your own machine).
>
> Good luck,
>
> Peter
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