I guess what I mean then is how are the edges assigned in the graph? When you do something like:
>>> G[exon1][exon2] = some_edge what is 'some_edge'? Is it an index? Is it an object created from the database? How does the Graph object know that there is an edge between exon1 and exon2, just by creating Graph(sourceDB=exonDB, targetDB=exonDB, edgeDB=spliceDB)? Thanks! On Jul 22, 9:49 pm, Christopher Lee <[email protected]> wrote: > Hi Kenny, > it's really a question of what you want to save as edge information. > If you just want to save one number, that can be saved trivially in > the Graph (via pickling if it gets saved to a shelve file), in the way > I outlined in my last email. If you want the edge information to be > something that itself is part of a database, then give the Graph an > edgeDB argument in the usual Pygr pattern... > > Example: we like to represent alternative splicing as a directed graph > whose nodes are exons and whose edges are splices. Exons are > annotations on the genome; splices are objects that give quite a bit > of info about that splicing event. We store the exons in a database > (in our case SQLTable). We also store the splices in a database (also > SQLTable). Then we create the graph as Graph(sourceDB=exonDB, > targetDB=exonDB, edgeDB=spliceDB). > > But if all you want to store as the edge-info is an int, creating an > edgeDB is overkill... > > -- 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 -~----------~----~----~----~------~----~------~--~---
