Thanks for the tips! - Changed strand to orientation in my Gene class, as you pointed out - Saved AnnotationDB to worldbase as well
Once genes_db was saved to worldbase, I did not have any problems loading the NLMSA object. And also didn't run into any pickling problems for my Gene and other classes. rochak On Jul 16, 1:00 pm, Christopher Lee <[email protected]> wrote: > 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 -~----------~----~----~----~------~----~------~--~---
