weiju/cmonkey-python — pull request #1 by jashworth-isb (2012-03-23 22:23:26+00:00)
Title: tps (T. pseudonana) integration, +messages, utils

I have added support for tps (T. pseudonana) in my fork. This involves the use of some manually-constructed data that are not available in remote databases.

I added to the sequence utilities so that they can be used to manually create upstream and downstream sequence files from the genome and gene models.

I have also added a few helpful messages.

I've added a vim modeline to the tops of the .py files so that my editor automatically adheres to the indentation style of the original repo.

Please review these diffs and incorporate those which belong in the core repo. I have not written a test for tps.py itself because I would like to use an existing example, say for leischmania.py, which I did not find.

Let me know if anything looks strange as I am relatively new to GitHub and this is my first pull request.

Thanks,
Justin