On Aug 27, 2009, at 3:09 PM, Paul Rigor (gmail) wrote: > In our group, we're using UCSC's Genome Browser (BED/BEDgraph) and > GBrowse-based browsers for viewing genomic features. We basically > have two sets of databases which are SQLTable-compatible for pygr > and another GFF3-compatible for GBrowse use.
Hi Paul, I'm not sure if this exactly fits your need, but Pygr 0.8 added MapView and GraphView classes, which enable you to execute arbitrary SQL (over multiple tables if you want) as the back-end for providing a one-to-one mapping (MapView) or many-to-many mapping (GraphView). And I suppose we could add a "SQLView" class that would provide a "view"- based analogue of the standard SQLTable class. The obvious downside to views across multiple tables is that the server-side JOIN requirement can make them slow... > > The advantage of SQLTable is that it works on a 'single > table' (simplicity) whereas GFF schema data is linked across > multiple tables. We could extend the SQLTable class to specify the > GFF 'source' attribute though and resolve the corresponding links to > GFF's data table. Could you explain what you mean in more detail? I don't know anything about GFF... > > 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? -- 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 -~----------~----~----~----~------~----~------~--~---
