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

[Cyrus Maher]

Thanks for your feedback, guys!! I did a bit of general clean-up and I've
made all the recommended PEP8 changes, with the exception that I kept
capital letters if they were part of an acronym. I've also switched the
link in the documentation over to github and configured mosaic to use the
MSAProbs application wrapper if it's installed. Let me know what you think!!

Docs: https://dl.dropboxusercontent.com/u/43327584/html/index.html
Code: https://github.com/cyrusmaher/mosaic

Cheers,

-Cyrus


On Tue, Aug 20, 2013 at 4:36 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
>
>
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