[Biopython-dev] [Bug 2880] Two unit tests issues in 1.51b (t-coffee and mafft)

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2880





------- Comment #4 from mmokrejs at ribosome.natur.cuni.cz  2009-07-18 14:41 EST -------
# python run_tests.py test_TCoffee_tool.py
test_TCoffee_tool ... ok
----------------------------------------------------------------------
Ran 1 test in 3.627 seconds

# t_coffee

PROGRAM: T-COFFEE (Version_7.54)
-full_log       S       [0] 
-run_name       S       [0] 
-mem_mode       S       [0]     mem
-extend         D       [1]     1 
-extend_mode    S       [0]     very_fast_triplet
-max_n_pair     D       [0]     10 
-seq_name_for_quadruplet        S       [0]     all
-compact        S       [0]     default
[cut]
# t_coffee -version
PROGRAM: T-COFFEE (Version_7.54)
# python run_tests.py test_Mafft_tool.py
test_Mafft_tool ... FAIL
======================================================================
FAIL: Simple round-trip through app with clustal output
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/var/tmp/portage/sci-biology/biopython-1.51b/work/biopython-1.51b/Tests/test_Mafft_tool.py",
line 78, in test_Mafft_with_Clustalw_output
    self.assert_(stdout.read().startswith("CLUSTAL format alignment by MAFFT"))
AssertionError

----------------------------------------------------------------------
Ran 1 test in 1.598 seconds

FAILED (failures = 1)
# python setup.py test
[cut]
test_Seq_objs ... ok
test_SubsMat ... ok
test_SwissProt ... ok
test_TCoffee_tool ... ok
test_UniGene ... ok
test_UniGene_obsolete ... ok
test_Wise ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
test_align ... ok
test_geo ... ok
test_interpro ... ok
test_kNN ... ok
test_lowess ... ok
test_pairwise2 ... ok
test_prodoc ... ok
test_property_manager ... ok
test_prosite ... ok
test_psw ... skipping. Install Wise2 (dnal) if you want to use Bio.Wise.
test_seq ... ok
test_translate ... ok
test_trie ... ok
test_triefind ... ok
Bio.Seq docstring test ... ok
Bio.SeqRecord docstring test ... ok
Bio.SeqIO docstring test ... ok
Bio.SeqIO.QualityIO docstring test ... ok
Bio.SeqIO.AceIO docstring test ... ok
Bio.SeqUtils docstring test ... ok
Bio.Align.Generic docstring test ... ok
Bio.AlignIO docstring test ... ok
Bio.AlignIO.StockholmIO docstring test ... ok
Bio.Application docstring test ... ok
Bio.KEGG.Compound docstring test ... ok
Bio.KEGG.Enzyme docstring test ... ok
Bio.Wise docstring test ... ok
Bio.Wise.psw docstring test ... ok
Bio.Motif docstring test ... ok
Bio.Statistics.lowess docstring test ... ok
======================================================================
FAIL: Simple round-trip through app with clustal output
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_Mafft_tool.py", line 78, in test_Mafft_with_Clustalw_output
    self.assert_(stdout.read().startswith("CLUSTAL format alignment by MAFFT"))
AssertionError

----------------------------------------------------------------------
Ran 123 tests in 342.671 seconds

FAILED (failures = 1)
#

So this time t_coffee test passed, sorry for the noise. I will try to find time
next week to upgrade mafft. Thanks.


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