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

[Christian Brueffer]

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