[Biopython-dev] [Bug 2051] XML Blast parser unusable with multiple queries and recent (2.2.13) blast - patch attached

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Dec 14 23:48:37 UTC 2006


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
             Status|NEW                         |ASSIGNED

------- Comment #9 from biopython-bugzilla at maubp.freeserve.co.uk  2006-12-14 18:48 -------
I've just checked in a fairly big change to Bio/Blast/NCBIXML.py (see revision
1.8), see bug 1970 comment 15.

NOTE: While it still reads an entire XML file in one go,
NCBIXML.BlastParser.parse() now returns a list of records - not a single record
as before.

This SHOULD address most of this bug (the unusable with multiple queries bit

Some of Jacob's suggestions in comment 1 have been included (e.g. the
expectation threshold parameter is dealt with more sensibly) but not all...

Could you test the new code please Jacob, and point out any outstanding issues.

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