[Biopython-dev] [Bug 3043] test_NCBI_BLAST_tools fails

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3043





------- Comment #7 from mdehoon at ims.u-tokyo.ac.jp  2010-05-07 07:39 EST -------
(In reply to comment #6)
> However the tool will not output XML in this mode, and it seems right
> now we can't parse the plain text output. Tabular output should be fine.

I'll put together a Blast output parser after Biopython 1.54 final is out.

> Could you run this test using the latest code?

THis works fine now. Thanks!

$ python test_NCBI_BLAST_tools.py
Check all blastn arguments are supported ... ok
Check all blastp arguments are supported ... ok
Check all blastx arguments are supported ... ok
Check all psiblast arguments are supported ... ok
Check all rpsblast arguments are supported ... ok
Check all rpstblastn arguments are supported ... ok
Check all tblastn arguments are supported ... ok
Check all tblastx arguments are supported ... ok
Pairwise BLASTP search ... ok
Pairwise BLASTN search ... ok

----------------------------------------------------------------------
Ran 10 tests in 0.389s

OK


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