[Biopython-dev] Plain text BLAST parser updated

Peter biopython at maubp.freeserve.co.uk
Tue Oct 20 15:08:55 UTC 2009

On Tue, Oct 20, 2009 at 2:24 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Tue, Oct 20, 2009 at 11:47 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> Hi all,
>> Just to let you know I've been doing a little work on the NCBI plain
>> text parser, and got it to work on multiquery output from recent
>> versions of BLAST (Bug 2090).
>> http://bugzilla.open-bio.org/show_bug.cgi?id=2090
>> I would not describe the changes as elegant, but the plain text parser
>> has evolved over time to cope with more and more NCBI variations, so
>> some ugliness is perhaps to be expected.
>> If there are any regressions, please report them and we can extend the
>> test suite. Likewise, if you have an recent plain text BLAST files
>> which didn't work and still don't work - get in touch, it may be easy
>> to fix.
>> [I'd still encourage everyone to use the XML output by default, but
>> there are times when the plain text is the only or best option.]
>> Peter
> The irony of this isn't lost on me. An hour after fixing the parser
> and testing it with BLAST 2.2.21 output, the NCBI made a release
> which broke it again.
> The output from the latest "classic" blastall 2.2.22 is fine.
> The output from the "new C++" blastx 2.2.22+ (and likely the
> other tools like blastp etc which are all separate executables
> now) breaks our plain text parser.

Touch wood, that is now working with the latest code in the public
repository. It really needs a few more example files covering more
than just the new blastx output...


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