[pygr-notify] Issue 74 in pygr: undefined 'al' in NLMSA.add_aligned_intervals

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Status: New
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Labels: Type-Defect Priority-Medium

New issue 74 by bpederse: undefined 'al' in NLMSA.add_aligned_intervals
http://code.google.com/p/pygr/issues/detail?id=74

hi, here's a test script which i believe shows a bug in latest pygr from
git://repo.or.cz/pygr:

{{{

from pygr import seqdb, cnestedlist
msa = cnestedlist.NLMSA('s', mode='memory',
                 pairwiseMode=True, bidirectional=True)
msa.add_aligned_intervals(alignedIvals=[], alignedIvalsAttrs={})

}}}

even when given real args for alignedIvals and Attrs, the al never exists
so it always fails.
http://repo.or.cz/w/pygr.git?a=blob;f=pygr/nlmsa_utils.py;h=25c07efb13dcbdb08e7c2ac12c6de5334c544a1a;hb=HEAD#l355


i can get around it by specifying a srcDB and destDB

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