[Biopython-dev] pypaml

[Brad Chapman]

Brandon;

> I've been toiling away on the PAML API and I think it's finally ready
> for review. If anyone's willing to give my code a review, here's my
> branch:
> https://github.com/brandoninvergo/biopython/tree/paml-branch

This is awesome; thanks much for all the work getting this together.
It's really great to see the extensive tests. I'm also impressed
with your story of porting over 'goto' statements; it's been a while
since those have entered my mind:

10 PRINT "CHI SQUARE FOREVER"
20 FLASH
30 GOTO 10

A couple of more general thoughts about your code:

- These looks to be a lot of shared functionality between codeml,
  baseml and yn00 in setting up the control files. Would it be
  possible to create a base class that these all inherit from? This
  would make the code much easier to maintain over time as formats
  change.

- Your 'read' functions get pretty deeply nested, especially the
  codeml parser. What do you think about creating an internal class
  to split some of the parsing logic into individual functions? A
  nice example is the GenBank/Scanner.py code. Having functions like
  parse_header/parse_features makes it much easier for someone not
  deeply familiar with your code to start to make guesses at where
  different functionality exists. This way, if the format changes
  others can provide patches and feedback to you.

Overall this is great and all the work is much appreciated.
Brad