hi, with the script pasted here:
http://pastebin.ca/1373633
everything runs fine when i dont pull the data loaded from pygr.Data,
and instead get it by building the NLMSA.
when i do try to get from pygr.Data, i get the error pasted at the end
of this email (and in the script).
how can i stop that error from occurring? (and use pygr.Data)
also, i have a couple of questions labelled "Q:" in the script, where
i'm not sure if i'm using pygr to full advantage.
so any pointers on that, and in general would be appreciated.
eventually, i want to use the items in the sorghum_anno (an
AnnotationDB) to query the NLMSA (named msa).
are the last 2 lines of the script the proper way to do that? it
works, but i think i need to use msa.addAnnotation()
to get sorghum/maize genes for a particular region as well--is that true?
so the specific question there is can i add annotations to the NLMSA
which i've created using NLMSA.add_aligned_intervals?
thanks,
-brent
===========================================
Traceback (most recent call last):
File "msorg.py", line 96, in <module>
for item, edge in msa[union_seq['sorghum.10'][1:40400]].items():
File "cnestedlist.pyx", line 1658, in pygr.cnestedlist.NLMSA.__getitem__
File "/usr/lib/python2.5/site-packages/pygr/nlmsa_utils.py", line
127, in __getitem__
seqID=self.getSeqID(seq) # USE SEQ ID TO LOOK UP...
File "/usr/lib/python2.5/site-packages/pygr/nlmsa_utils.py", line
139, in getSeqID
return (~(self.nlmsa.seqDict))[seq]
File "/usr/lib/python2.5/site-packages/pygr/seqdb.py", line 570, in
__getitem__
if anno_seq_attr.db in self.db.dicts:
AttributeError: 'NoneType' object has no attribute 'db'
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