[Biopython-dev] New BioPython member

[Peter Cock]

On Tue, Jan 29, 2013 at 9:22 PM, Nate Sutton <natemsutton at yahoo.com> wrote:
> Dear all,
>
> I just recently joined the BioPython developers group and am
> looking forward to contributing to BioPython!  I have worked for a while
> in programming, genetics, and biology and have
> a m.s. in Biomedical Informatics.  After
> talking with some fellow contributors I have decided to try working on
> https://redmine.open-bio.org/issues/3360 but I will also work on writing
> some documentation on examples from the
> cookbook, especially if I am stuck on the bug.  If anyone wants to work on
> the same things, I’d be glad to hear that, I
> may be slow on the work because I am still learning Python after coming
> from
> other languages.
>
> -Nate

Hi Nate, and welcome.

Eric is in charge of the Bio.Phylo module, but within that the
command line application wrappers under Bio.Phylo.Applications
follow a pattern used elsewhere in Biopython.

To add a wrapper for fasttree http://www.microbesonline.org/fasttree/
have a look at the existing wrappers for PHYML and RAXML, defined in
Bio/Phylo/Applications/_Phyml.py and Bio/Phylo/Applications/_Raxml.py
(leading underscores mean private modules in Python), which are
exposed to the user via Bio/Phylo/Applications/__init__.py

In this case, I'd suggest putting the new wrapper in a new file,
Bio/Phylo/Applications/_fastree.py

Other similar wrappers existing under Bio.Emboss, Bio.Align, etc.

Don't be shy about asking for guidance on this, or git and github.
Ultimately I'm hoping you'll be able to do is take a fork (personally
copy of the repository) on GitHub, create a new fasttree branch,
commit your enhancements, and make a pull request. If that's
all too much for now, simply writing the new file and letting us
do the git side would be fine.

Regards,

Peter