The documentation for pygr is written in dense bioinformatics-speak. I certainly understand why, but it would be useful for those of us outside that community if there were some dirt-simple examples, too. I've been looking at it as a graph database implementation, comparing it with neo4j, for use with my personal digital library system, UpLib. The things I needed to know were:
1. out-of-the-box, it uses the btree system in bsddb for efficient disk access. Which, as another poster noted, doesn't work out-of-the- box on OS X. Use of bsddb has been a long-standing breakage issue with Python; that's why it was removed in 2.6. It's perceived as impossible to provide stable support for. 2. the GraphQuery class is not in the pygr.mapping module, despite what the documentation says. 3. you build a graph by instantiating an instance of either Graph or dictGraph, and adding nodes and edges to that instance. Once I'd ferreted those facts out of the docs, I was up and running. --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
