[pygr-notify] Issue 116 in pygr: schema binding gives an integer key error

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Status: New
Owner: pygr-bug... at googlegroups.com
Labels: Type-Defect Priority-Low

New issue 116 by deepreds: schema binding gives an integer key error
http://code.google.com/p/pygr/issues/detail?id=116

1. create directory "ucsc1"
2. get refGene.txt.gz at  
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ and save
into "ucsc1"
3. modify hg18 SequenceFileDB path in make_test.py (attached script)
4. run make_test.py in current directory (not "ucsc1" directory)

As far as I know, if we call attribute bound to SequenceFileDB (slice1.tu,  
bindAttrs = ('tu',)), it will
retrieve all annotations. it gives integer key error.

>>> import os
>>> os.environ['WORLDBASEPATH'] = '.'
>>> from pygr import worldbase
>>> worldbase.dir()
['0root', '0version', 'Bio.Annotation.UCSC.refGene.HUMAN.hg18.tus',
'Bio.MSA.UCSC.refGene.HUMAN.hg18.tus', 'Bio.Seq.Genome.HUMAN.hg18',
'SCHEMA.Bio.Annotation.UCSC.refGene.HUMAN.hg18.tus',
'SCHEMA.Bio.Seq.Genome.HUMAN.hg18',
'__doc__.Bio.Annotation.UCSC.refGene.HUMAN.hg18.tus',
'__doc__.Bio.MSA.UCSC.refGene.HUMAN.hg18.tus', '__doc__.Bio.Seq.Genome.HUMAN.hg18']
>>> hg18 = worldbase.Bio.Seq.Genome.HUMAN.hg18()
>>> tus = worldbase.Bio.Annotation.UCSC.refGene.HUMAN.hg18.tus()
>>> msa = worldbase.Bio.MSA.UCSC.refGene.HUMAN.hg18.tus()
>>> slice1 = hg18['chrY'][:500000]
>>> edges = msa[slice1].edges()
>>> len(edges)
4
>>> edges
[(chrY[138060:160020], annot31862[0:21960], <pygr.sequence.Seq2SeqEdge  
object at
0x9ec4d0>), (chrY[161425:170887], -annot16267[0:9462],  
<pygr.sequence.Seq2SeqEdge
object at 0x9ec750>), (chrY[214969:222590], -annot2893[0:7621],
<pygr.sequence.Seq2SeqEdge object at 0x9ec810>), (chrY[214969:267627], -
annot3680[0:52658], <pygr.sequence.Seq2SeqEdge object at 0x9ec850>)]
>>> tus[31862]
annot31862[0:21960]
>>> slice1.tu
Traceback (most recent call last):
   File "<stdin>", line 1, in <module>
   File "/data/server/pygr/build/lib.linux-x86_64-2.5/pygr/metabase.py",  
line 61, in __get__
     result=targetDict[obj] # NOW PERFORM MAPPING IN THAT RESOURCE...
   File "/data/server/pygr/build/lib.linux-x86_64-2.5/pygr/annotation.py",  
line 167, in
__getitem__
     return self.sliceAnnotation(k,self.sliceDB[k])
   File "/data/server/pygr/build/lib.linux-x86_64-2.5/pygr/mapping.py", line  
395, in __getitem__
     return self.d[self.saveKey(k)]
   File "/data/server/pygr/build/lib.linux-x86_64-2.5/pygr/mapping.py", line  
387, in saveKey
     raise KeyError('IntShelve can only save int or str as key')
KeyError: 'IntShelve can only save int or str as key'



Attachments:
	make_test.py  2.3 KB

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