[Biopython] OrthoXML parser?

[Eric Talevich]

Hi guys,

Biopython has SeqXML support in SeqIO in recent releases thanks to Thomas
Schmidt. We don't parse OrthoXML yet, mainly because there's no special
support for ortholog groups as an object type yet in Biopython. But you can
get the raw information from an OrthoXML file using the ElementTree module:
http://docs.python.org/2/library/xml.etree.elementtree.html

Cheers,
Eric



On Fri, Jun 14, 2013 at 10:33 AM, Philipp Schiffer <
philipp.schiffer at gmail.com> wrote:

> Hi!
>
> Thanks a lot (actually should have seen this myself). Just checked out the
> latest (I think) biopython from git, but only seem to find SeqXML there:
> - seqxml  - SeqXML, simple XML format described in Schmitt et al (2011).
> But no OrthoXML. Or am I not seeing it?
>
> Best
>
> Philipp
>
> --
> Philipp Schiffer
> Sent with Sparrow (http://www.sparrowmailapp.com/?sig)
>
>
> On Friday, 14. June 2013 at 16:08, Nick Lindberg wrote:
>
> > Looks like there is a patch for Biopython that will give you OrthoXLM and
> > SeqXML support, but you'll have to do it yourself:
> >
> > http://seqxml.org/xml/Biopython_Old.html
> >
> >
> > Perhaps it's already in the latest release? I'm not at my machine so I
> > can't check.
> >
> > Nick Lindberg
> > Sr. Consulting Engineer, HPC
> > Milwaukee Institute
> > 414.727.6413 (W)
> > http://www.mkei.org
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > On 6/14/13 5:36 AM, "Philipp Schiffer" <philipp.schiffer at gmail.com(mailto:
> philipp.schiffer at gmail.com)> wrote:
> >
> > > Hi there!
> > >
> > > Does anybody now if there is a module to parse the OrthoXML format
> > > in/with biopython?
> > >
> > > Thanks
> > >
> > > Philipp
> > >
> > > --
> > > Philipp Schiffer
> > > Sent with Sparrow (http://www.sparrowmailapp.com/?sig)
> > >
> > >
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> > >
> >
> >
> >
>
>
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