Hi, a few initial comments: - your Gene class is used solely as the "slice info" for *constructing* an annotation object, so leave the AnnotationDB.itemClass as the default (AnnotationSeq).
- Since you're not using Gene to create interesting object-oriented behaviors, I suggest you just use a tuple, which eliminates any possible problems with pickling your Gene class. You can do that as follows: genes_db = seqdb.AnnotationDB(genes, sorghum, annotationType='Gene:', sliceAttrDict=dict(id=0, start=1, stop=2, orientation=3)) The sliceAttrDict tells AnnotationDB the order of the required slice info attributes in each tuple. Then add your gene info as tuples to the genes dictionary, like so: genes[name] = (seqID, start, stop, strand) - first make sure that you can retrieve gene annotations successfully from gene_db, then make sure you can query genes_map successfully with sequence regions to find the appropriate gene annotations, then *finally* try saving this in worldbase. It is much easier to debug one thing at a time, before adding the extra complications of unpickling / worldbase. For example, it doesn't look like your Gene code would work as written, because AnnotationDB expects the orientation attribute to be called "orientation" but Gene saves it as "strand"... - you saved the NLMSA to worldbase, but apparently didn't save the AnnotationDB to worldbase. You should save that to worldbase too. Hope this helps... -- Chris Lee --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
