[Biopython-dev] New BioPython member

[Nate Sutton]

Thanks for the welcome!  Also, I looked briefly through the code with the files you wrote about and I see the command line app wrapping components you described.  I appreciate the advice about how the do the wrapper and I am glad to know of that pattern of command line app wrapping that is consistent with code in other places of BioPython.  Thanks for the other advice including possibly asking for guidance.  I’ll just give it a shot and hopefully things go smoothly but it being my first BioPython coding I appreciate the support.

Thanks,

Nate


________________________________
 From: Peter Cock <p.j.a.cock at googlemail.com>
To: Nate Sutton <natemsutton at yahoo.com> 
Cc: "biopython-dev at lists.open-bio.org" <biopython-dev at lists.open-bio.org> 
Sent: Wednesday, January 30, 2013 2:31 AM
Subject: Re: [Biopython-dev] New BioPython member
 
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