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

[Cyrus Maher]

Thanks for sending that along Lenna! And thanks everybody for being patient
with me! This is my first experience sharing software, so it's great to
learn from you guys...

As far as updates:
-I've fixed all pep8 errors, with the exception of some finicky
continuation indent complaints.
-I've also uploaded example files so that the file "mosaic_example.py" can
be run without modification. From the mosaic directory, just type:
    python mosaic_example.py testfiles.txt
-The documentation has be updated as well.

I would of course be open to any additional feedback you guys could offer
for improving the code.

That said, I was also hoping to get your thoughts on whether this seemed
like the type of project that would fit in with Biopython. Peter said that
Eric might have some good comments on this matter?


Cheers,

-Cyrus




On Tue, Aug 20, 2013 at 2:31 PM, Lenna Peterson <arklenna at gmail.com> wrote:

> 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
> >
> >
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> > http://lists.open-bio.org/mailman/listinfo/biopython-dev
> >
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