Hi, in the interest of making pygr easier to understand and work with, I've tried to subdivide large modules (such as seqdb) into smaller, more coherent pieces. For example, I recently moved all the BLAST support out of seqdb.py into a new module blast.py.
Perhaps we should also move annotation functionality out of seqdb into a new module (annotate.py or annotation.py?). AnnotationDB doesn't depend on seqdb; I don't think the prospective annotation.py would even need to import seqdb... Their association is purely conceptual. One consideration: backwards compatibility for unpickling and thus pygr.Data. Unpickling looks for classes based on the module location saved when the object was originally pickled, so to maintain the ability to unpickle (e.g. retrieve from pygr.Data) existing annotation resources, we'd have seqdb import a few key classes (AnnotationDB and kin) from annotation.py, so that those names continue to be accessible from the seqdb namespace as before. What do you think? Does this seem worthwhile, and should we include this in the 0.8 release? Yours, Chris --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
