[Biopython] SeattleSeq type library

[Peter Cock]

On Wed, Feb 9, 2011 at 9:42 PM, Adrian Johnson
<oriolebaltimore at gmail.com> wrote:
> Dear group,
>
> Is there a library in biopython that takes a pileup file as an input
> and  processes the file and  gives back an output with annotations
> with gene name, NM accession, mutation type and type of change
> (splice site, coding etc) and many other details related
> to protein and gene sequence.

No, nor a parser for the related mpileup format. Would you like to
write something?

>
> I use SeattleSeq Annotation and the limitation is that it is a web based tool
> and limits the ability to use it in a pipeline. I am interested in similar tools
> that can be used through a command line parameters.
>

Is working with GFF3 files an option? Brad has from GFF code we hope
to integrate into Biopython shortly (available now as an extra install).

>
> The ideal situation would be a BioPython module that uses SOAP interface
> to either NCBI or UCSC.
>

Which SOAP interface? There are lots of them...

How about the NCBI Entrez REST API? See our Bio.Entrez module.

Peter