Hi!
First of all, pygr is awesome. Thanks heaps to the developers. It is
a big help.
I'm new to pygr. I'm trying to build a pygr resource of exons over
the entire genome. I have a resource of all the genes, plus a
SQLTable with the exon information in UCSC's refseq form:
column exonStarts
1213042,1213331,1214185,1214333,1216053,1216285,1216467,1216790,1216945,1217383
column exonEnds
1213278,1213396,1214280,1214485,1216222,1216416,1216717,1216888,1217103,1217466,
I build a Collection of exons by zipping together each of the starts
and ends.
Right now, my code builds a mapping from genome to exon using
annotation_db = annotation.AnnotationDB(exonCollection, genome,
filename=opts.path_stem+'_exons',mode='cw')
annotation_map = cnestedlist.NLMSA(pathstem=opts.path_stem,
mode='w',
pairwiseMode=True,
bidirectional=False)
for event in annotation_db.itervalues():
annotation_map.addAnnotation(event)
annotation_db.__doc__ = 'annotation database for exons of %s' %
opts.genome_resource
annotation_map.__doc__ = 'annotation map for genome-> exons of %s' %
opts.genome_resource
pygr.Data.addResource(db_resource_string, annotation_db)
pygr.Data.addResource(map_resource_string, annotation_map)
pygr.Data.ManyToManyRelation(genome,annotation_db,bindAttrs=
('annotation_db',))
pygr.Data.save()
There is other code that creates the OneToMany Mapping of gene->exons,
which is also suffering, but I thought I'd start out here. When I try
to load the resulting resource, I'm getting
<type 'exceptions.AttributeError'>: FakeModule object has no attribute
'Exon'
The Exon class is defined above this, and the ExonCollection uses
Collection(itemClass=Exon).
I'm not sure where the problem is...
The source is posted at http://pastebin.com/m42d7a159
Thanks!
Jake Biesinger
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