[Biopython-dev] COMPASS parsing code
chapmanb at uga.edu
Wed May 5 06:32:31 EDT 2004
> I have written some code for parsing compass results.
> I have attached the code, which you might like to include in the biopython
Thank you! I just checked this code into Bio/Compass/__init__.py.
There are a few adjustments based on your points below but basically
it is as submitted. Please let me know if I messed anything up.
> There are probably a few issues with the code that could make it better:
> * the unit tests use some sample input, file comtest1 and comtest2. These are
> just read using open. I have seen someone use test.locate or something like
> that, but I'm not sure how that works. If you want to enlighten me, I'll
> change it.
Biopython has it's own test system in the Tests directory, which
allows us to run all of the tests at once. It is documented pretty
I converted your code over to this system (thanks for using
unittest, by the way) and it is located in Tests/test_Compass.py
with the input files in Tests/Compass/.
> * i have used regular expressions inefficiently, as I'm not sure how you're
> supposed to cache them using the _Scanner/_Consumer framework. At the moment
> each subroutine compiles an re when called, which can't be good. Again,
> please enlighten me to a better way and I will change it.
I just made the compiled regular expressions attributes of the
_Scanner class. This way they should only be compiled a single time
when a class is first instantiated, and then will be used when the
functions are called during the scanning. I think this will make
things a little more efficient, although I am certainly no regular
expressions expert myself.
Thanks again for the contribution! Much appreciated.
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