[BioPython] Substitution matrices

[Jeffrey Chang]

> o  Can I parse the standalone blastpgp output directly from an output
>    file which is the result from a run _not_ via biopython? Code example?

Yes.  I'll bet that the majority of the output that has been parsed with
the parser was not generated by biopython.  Anyways, biopython provides a
very simple interface to blastpgp that just passes its parameters through,
without doing anything fancy with the output.

A warning, though...  The parser is pretty strict, and rejects anything
that's not from the standard psiblast!  :)

Here's a snippet of code that parses output from the 'bt009' blast test.


>>> from Bio.Blast import NCBIStandalone
>>> parser = NCBIStandalone.PSIBlastParser()
>>> rec = parser.parse(open('bt009'))                                
>>> print rec.converged
1     
>>> print len(rec.rounds)
2
>>> 



Jeff