[Biopython-dev] MAF Parser/Indexer

[Andrew Sczesnak]

Hi Brad,

Thank you for the feedback. I've tried to work on some of your 
suggestions and will continue doing so.

> - Could you refactor some of the larger functions into separate smaller
>    components? A couple of these spread over a ton of lines and it can be
>    a bit difficult to follow the logic throughout:

Definitely--I see what you mean. I split __init__ into a couple 
functions. I'm still worried about the 100 lines of get_spliced(). It's 
big mostly because I overdid it on the comments, but hopefully that 
helps explain the logic enough that someone else could work on it 
without pulling their hair out.

> - Would you be able to put together a small example for the
>    Cookbook or Tutorial documentation? This would be a great way to help
>    others get started with the functionality and advertise it.

Absolutely. I have a few more ideas for cool demos that integrate with 
other parts of Biopython. What's the best place to put draft text for 
the tutorial?


Thanks,
Andrew