[Biopython-dev] [Bug 2361] Test Suite Failures

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

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





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2007-09-11 16:23 EST -------
You seem to be the bearer of bad news :(

My first impression is that you are right in that mxTextTools 3.0 is to blame:
http://www.egenix.com/products/python/mxBase/mxTextTools/changelog.html

e.g. from their changes from 2.0.3 to 3.0.0
> Restructured tag commands and their numbering so that
> low-level commands come before the special ones. Old
> tag tables need to be "recompiled" due to this change!

If you can still download mxTextTools 2.x.x from their website, its not at all
obvious.

As to the impact in Biopython, most of the unit tests failures are clearly
problems in Biopython's Martel library and/or the python Sax library:

test_CodonUsage - depends on Bio.Fasta which depends on Martel
test_Fasta2 - depends on Martel
test_KEGG - depends on Martel
test_align - depends on Bio.Fasta which depends on Martel
test_format_registry - depends on Martel
test_geo - depends on Martel
test_Fasta - unclear from the error, but known to depend on Martel
test_GenBankFormat - depends on Martel
test_NNGene - failure unclear
test_SCOP_Astral - failure unclear

Most of these Martel based parsers are less commonly used (IMO), which the
exception of Bio.Fasta where at least removing the Martel dependance would be
fairly easy.


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