[Debian-med-packaging] BioPython unit tests: Mafft

[Andreas Tille]

[Bouncing my mails to Peter Cock since spam means rejected my mails,
 sorry Peter, just let me know how to at best report bugs preferably
 via mail]

Hi,

I try to activate all possible tests of BioPython at Debian package
build time but I found some issues.  I will discuss these in separate
mails, continuing with test_Mafft_tool and python2.7:

======================================================================
FAIL: test_Mafft_simple (test_Mafft_tool.MafftApplication)
Simple round-trip through app with infile.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/buildd/python-biopython-1.65+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_Mafft_tool.py", line 86, in test_Mafft_simple
    self.assertTrue("Progressive alignment ..." in stderrdata, stderrdata)
AssertionError: 
nseq =  3
distance =  ktuples
iterate =  0
cycle =  2
sparsepickup = 0
nguidetree = 2
nthread = 0
sueff_global = 0.100000
generating a scoring matrix for nucleotide (dist=200) ... done
done
done
scoremtx = -1
Gap Penalty = -1.53, +0.00, +0.00

tuplesize = 6, dorp = d


Making a distance matrix ..

There are 89 ambiguous characters.

    1 / 3
done.

Constructing a UPGMA tree ... 

    0 / 3
done.

Progressive alignment 1/2... 

STEP     1 / 2 f
STEP     2 / 2 d
done.

Making a distance matrix from msa.. 

    0 / 3
done.

Constructing a UPGMA tree ... 

    0 / 3
done.

Progressive alignment 2/2... 

STEP     1 / 2 f
STEP     2 / 2 d
done.

disttbfast (nuc) Version 7.245 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
0 thread(s)


Strategy:
 FFT-NS-2 (Fast but rough)
 Progressive method (guide trees were built 2 times.)

If unsure which option to use, try 'mafft --auto input > output'.
For more information, see 'mafft --help', 'mafft --man' and the mafft page.

The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
It tends to insert more gaps into gap-rich regions than previous versions.
To disable this change, add the --leavegappyregion option.



Unfortunately I have no idea how to deal with this.  Any hint?

Kind regards

        Andreas.

-- 
http://fam-tille.de