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

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Comment #7 on issue 40 by cjlee112: add NLMSA convenience method for  
loading aligned intervals from any source
http://code.google.com/p/pygr/issues/detail?id=40

In answer to Titus' question about CoordsGroupStart / End:
BLAST returns alignments one at a time.  A given alignment might contain  
any number
of aligned interval pairs.  For some alignment results (tblastn, blastx,  
tblastx),
the grouping of the interval pairs into a single alignment is crucial  
information.
CoordsGroupStart indicates the beginning of a BLAST alignment;  
CoordsGroupEnd
indicates the end of an alignment.  Search on CoordsGroupStart in blast.py  
to see
examples of how this is used, if you're interested.

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