Python module for DAWG - PyDawg

[zmertens]

Putting up this PR to keep track of changes and progress for making a Python module for DAWG.

• Overall goal right now is to have a Python module that makes it easy to express DAWG tricks in a Pythonic way
• Right now most of the work is being done through Cython, but there is also a SWIG and Boost.Python module with working examples. The brief analysis is done in the Dawg_Python_Analysis.md
• Other ideas:
  • Take advantage of BioPython modules for formatting
  • Generator expressions for iterating over sequence details?

[dng-jenkins]

Can one of the admins verify this patch?

[zmertens]

@anderspitman Here is the work on the DAWG Python wrapper.

• The GoldenRetriever.py was the first set up that doesn't use any BioPython (it is just a wrapper around DAWG's IO and evolver/alignment functions).
• The Akita.py is a bit more loyal to BioPython.

Still working on Greyhound.py which will try to be faster than the pure C++. That's the dream.

[zmertens]

Time for 1000 runs using the time_akita.sh script:

PyDawg - Akita
real        2m8.856s
user       1m58.667s
sys         0m8.500s

Pure CPP Dawg
real        0m0.364s
user       0m0.013s
sys        0m0.103s

[dng-jenkins]

Can one of the admins verify this patch?