On Thu, Aug 27, 2009 at 03:35:41PM -0700, Christopher Lee wrote: -> > By the way, we have several in-house tools for generating annotation -> > databases from csv files: from cvs -> sql table -> pygr annotatino -> > db. Could these tools be incorporated into pygr? -> -> csv is a standard format, and if bioinformatics people are already -> using it widely, it would make sense for Pygr to be able to read those -> data conveniently. I guess it depends on whether your tools are -> reasonably general, or will only work for one specific application... -> Can you describe your tools a bit? -> -> Titus, what do you think?
Generic == good. I worry a bit about adding too many "data loading" scripts into pygr itself, though; every text format is slightly different, and a generic solution seems unlikely. I'd rather that we focus instead on adding useful public data sets to worldbase, AND providing plenty of examples of how to load stuff into pygr from various useful text data formats. Both would be great. Hmm, though, perhaps an adapter that lets you take a CSV DictReader with particular field names and turn it into annotations, and/or gives you a way to specify a callable to turn a row into a annotation information... that might be usefully generic. 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 -~----------~----~----~----~------~----~------~--~---
