[Biopython-dev] MUMmer

[Brad Chapman]

Marcin;

> I guess I should start with a nice 'hi' to everybody, now that I am
> sending my first message to this group. So: Hi, Everybody! 

Welcome. We are happy to have you.

> Now, that we have the formality out of the way, I will get to the point.
> Recently, I have written some Python code for parsing and processing the
> output of MUMmer tool (http://mummer.sourceforge.net/). More
> specifically, the code I have manages invocations and handles outputs of
> the nucmer pipeline (alignment of multiple closely related nucleotide
> sequences) and of mummer itself (short exact matches). Obviously, the
> results are ultimately rendered as pairs of biopython's Seq objects. 

This is great -- we don't have support for MUMmer alignments so this
is very welcome.

> I use this stuff only myself, in work on bacterial genomes, but I would
> be more than willing to contribute it to the project. It may be rough
> around the edges at the moment, but I think I could easily give it the
> necessary polish if there is interest in having it included. 

As Bartek mentioned, the first step is to organize the code you have
and start it as a branch on GitHub. Being able to see the code will
help us make specific suggestions. Generally, based on what you've
written it sounds like this will fit into the alignment interfaces.
Peter and Cymon have been working on organizing this. Support for
command lines and running programs lives in:

http://github.com/biopython/biopython/tree/master/Bio/Align/Applications

Parsing output and returning alignment objects is organized in the
AlignIO module:

http://github.com/biopython/biopython/tree/master/Bio/AlignIO
http://www.biopython.org/wiki/AlignIO

Tests are an important part of the submission process and many
examples are found here:

http://github.com/biopython/biopython/tree/master/Tests

test_Clustalw.py is an example of a print and compare style test,
and test_Mafft_tool.py is a unittest style test. We are more
concerned with good testing coverage then how exactly the tests get
written.

We can definitely help with more specific feedback but hopefully
this gives you a general idea to get started.

Looking forward to seeing the code,
Brad