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

[David Cain]

Hi, Cyrus - I took a quick look at your code on GitHub. Did you publish a
different version of MOSAIC? By my linter, there are 309 PEP8 errors on
mosaic.py.

Also, as a general comment, your code seems to rely on sys.exit
extensively. Python's exception framework is pretty handy - maybe your
module could raise its own custom exceptions (Biopython's PDB parser is a
good example of this design strategy).



David Cain
+1 (339) 222 4452


On Tue, Aug 20, 2013 at 2:24 PM, Cyrus Maher <michael.maher at ucsf.edu> wrote:

> 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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> >
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