[pygr-notify] Issue 40 in pygr: add NLMSA convenience method for loading aligned intervals from any source

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Updates:
	Status: Assigned

Comment #5 on issue 40 by the.good.doctor.is.in: add NLMSA convenience  
method for loading aligned intervals from any source
http://code.google.com/p/pygr/issues/detail?id=40

Initial review: created a new test class, ran code.

Issues:

fixed 'al.seqDict' bug

Also, the ori attribute was not optional for tuples without some mangling.   
See tests
and classutil fix.

In the docs, the names of the passed-in seqdbs are wrong: alignedIvalsSrc  
=> srcDB,

alignedIvalsDest => destDB.

I think for read_aligned_coords, alignedIvalsAttrs should default to {}.   
See the
weird pathological behavior in nlmsa_test, method test_single_ival_attr(),  
for a
reason why.

I don't understand the need for or use of CoordsGroupStart/End.  ??

See branch http://github.com/ctb/pygr/commits/review_issue40.


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