[Biopython-dev] [Bug 2090] Blast.NCBIStandalone BlastParser fails with blastall 2.2.14

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Mar 15 00:50:40 UTC 2007


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

           What    |Removed                     |Added
                 CC|                            |biopython-
                   |                            |bugzilla at maubp.freeserve.co.
                   |                            |uk

------- Comment #11 from biopython-bugzilla at maubp.freeserve.co.uk  2007-03-14 20:50 EST -------
> No, I haven't looked at this. Basically I have given up on
> parsing plain-text output from Blast. I don't think it can
> be done reliably. On the other hand, if the patch solves some
> of the issues with plain-text parsing, I'm all for it.

I agree with you that maintaining the plain-text parsing is a pain - especially
given the recent change for the output for multiple queries where the header is
no longer repeated.

However, the patch did help for parsing the output of single queries, which is
better than nothing.

Note that I haven't touched this code since December, but the only change in
CVS in the meantime was the trivial "oldengine" switch, so it should be easy to
merge this in.

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