[Biopython-dev] [Bug 2481] bitscore not parsed.

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2481





------- Comment #4 from sbassi at gmail.com  2008-04-05 01:24 EST -------
(In reply to comment #3)
> Isn't the bit score in the hsps?

Yes, it is. But this is not the only place it should be, keep on reading.

> Otherwise, which line in xbt001.xml is not being parsed?

This is not the problem (we are not missing a line from being parsed from the
xml). The problem is that "bit" is not in "description" as it should be. Why it
should be in description? Take this example:

>>> fr.alignments[0].hsps[0].expect
8.32193

But you also have "expect" in "descriptions":

>>> fr.descriptions[0].e
8.32193

Another example:

>>> fr.alignments[0].hsps[0].score
16.0

and

>>> fr.descriptions[0].score
16.0

"descriptions" corresponds to the description table in BLAST HTML documents,
all values from table should be there.


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