Hi!
Currently running pygr-0.8.0-py2.6-linux-x86_64 without PYGRDATAPATH
or WORLDBASEPATH set to anything.
trying the following:
from pygr import worldbase
msa = worldbase.Bio.MSA.UCSC.dm3_multiz15way()
tricas = worldbase.Bio.Seq.Genome.TRICA.triCas2()
seq = tricas['singleUn_263'][4110:6700]
Everything seems to have loaded fine. But
msa[seq]
is throwing an exception...
---------------------------------------------------------------------------
TypeError Traceback (most recent call
last)
/home/baldig/projects/genomics/nonsvn/output/fly/motifsearch/
2009_7_30_13_19_39_3_211_1/pipeline/stderr/<ipython console> in
<module>()
/home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/
python2.6/site-packages/pygr-0.8.0-py2.6-linux-x86_64.egg/pygr/
xnestedlist.pyc in __getitem__(self, k)
65 'directly call slice without any ID lookup -- will be
done server-side'
66 try:
---> 67 return cnestedlist.NLMSASlice(self.seqlist
[0],k.start,k.stop,-1,-1,k)
68 except EmptySliceError:
69 return EmptySlice(k)
/home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/
python2.6/site-packages/pygr-0.8.0-py2.6-linux-x86_64.egg/pygr/
cnestedlist.so in pygr.cnestedlist.NLMSASlice.__cinit__()
/home/dock/shared_libraries/lx64/pkgs/pythonsandbox/2.6.2/lib/
python2.6/site-packages/pygr-0.8.0-py2.6-linux-x86_64.egg/pygr/
xnestedlist.pyc in doSlice(self, seq)
58 elif result == 'EMPTY':
59 raise EmptySliceError
---> 60 id,l,d=result
61 for nlmsaID,(seqID,nsID) in d: # SAVE SEQ INFO TO
INDEX
62 self.seqs.saveSeq(seqID,nsID,0,nlmsaID)
TypeError: 'bool' object is not iterable
I know that at least part of the triCas sequence is in the msa:
In [13]: msa.seqDict.has_key('triCas2.singleUn_263')
Out[13]: True
Any ideas?
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