[Biopython-dev] Fwd: New Biopython (sub)module?

[Lenna Peterson]

Also worth noting is autopep8: https://pypi.python.org/pypi/autopep8
(it can be a bit aggressive but that's what version control is for, right?)

Cheers,

Lenna


On Tue, Aug 20, 2013 at 7:36 AM, Christian Brueffer
<christian at brueffer.de>wrote:

> On 8/19/13 21:24 , Cyrus Maher wrote:
> > Hi everybody!!-
> >
> > My name is (Michael) Cyrus Maher, and I'm a PhD student at UCSF in the
> lab
> > of Dr. Ryan D. Hernandez (http://bts.ucsf.edu/hernandez_lab/)...
> >
> > I am writing because I'm interested in submitting a new Biopython module.
> > Since this is likely a one-time event, the wiki recommends proceeding
> > through a developer. After speaking with Peter Cock, he recommended that
> I
> > open things up for discussion on the mailing list.
> >
> > Attached is a draft that describes a new method, termed MOSAIC, which
> > integrates multiple sequence alignments from an arbitrary number number
> of
> > sources. We show that it greatly increases the number of orthologs that
> we
> > are able to detect while maintaining or improving functional-,
> > phylogenetic-, and sequence identity-based measures of ortholog quality.
> >
> > Code and documentation may be found here:
> >
> > https://dl.dropboxusercontent.com/u/43327584/html/index.html
> >
> > Looking forward to hearing what you think!
> >
>
> Hi Cyrus,
>
> I agree with David on the PEP8 issue.  A very nice tool to use is the
> pep8 checker, https://pypi.python.org/pypi/pep8
>
> I see that you use MSAProbs.  I have an MSAProbs application wrapper in
> the works.  I haven't submitted it yet due to incomplete unit tests,
> but maybe it's useful to you:
>
> https://github.com/cbrueffer/biopython/tree/msaprobs
>
> Cheers,
>
> Chris
>
>
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython-dev
>