[Biopython-dev] [Bug 2361] Test Suite Failures from Martel/Sax with egenix mxTextTools 3.0

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http://bugzilla.open-bio.org/show_bug.cgi?id=2361





------- Comment #18 from mdehoon at ims.u-tokyo.ac.jp  2007-09-13 00:44 EST -------
On my computer, "python test_Fasta.py" does fail.
Three of the four tests in test_Fasta.py succeed, the fourth one
(DictionaryTest) fails. The error occurs in the index_file function in
Bio/Fasta/__init__.py, which is needed to create a Fasta.Dictionary. This code
is used to create your own Fasta database, along the lines of the Genbank
example in section 4.3.4 in the Tutorial. I think that this stuff can be done
more cleanly with the new Bio.SeqIO.

I'll ask on the Biopython mailing list if somebody is using index_file. If not,
we can deprecate only that function in Bio.Fasta, and remove the corresponding
test in test_Fasta.py.


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