On Mon, Jun 29, 2009 at 01:53:38PM -0700, David M. Goodstein wrote: -> We're just trying to build some annotation objects of a very general -> nature (Genes, AlignedESTs, AlignedShortReads) and the documentation -> seems to suggest these classes have to be created de novo (via -> subclassing ItemClass), and for example the mappings of exons to -> genes also has to be explicitly created. -> -> Since I doubt we are the first to want to work with these types of -> objects, I was wondering what is already out there floating around in -> terms of existing clases and/or creation scripts. -> -> thx, -> --David
Hi David, sorry, I just noticed that no one had responded to this... here is how I think Chris Lee handles this: pygr excels at wrapping things into object-like forms, and in particular it excels at wrapping SQL data. I get the impression that the majority of pygr work in the past was aimed at the UCSC data set, for which the annotations (genes, etc.) are available in SQL. So my guess is that Chris mostly uses the sqltable wrappers. I have a nice example or two somewhere but (of course) it is awaiting time for me to write it up. I have gone the route that you are proposing to go -- building my own classes -- once or twice. I've never produced anything re-usable, mainly because I was just learning pygr myself at the time; now I'd probably go the SQL-wrapping route ;) If you want SQL examples, let me know and I'll prioritize writing them up. cheers, --titus -- C. Titus Brown, [email protected] --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
