[Biopython] BioPython unit tests: Mafft

[Peter Cock]

Hi Andreas,

I'm not seeing any moderation requests but the biopython
lists are members only simply as otherwise we cannot cope
with the spam volumes. CC'ing me is a quick solution if
you prefer not to report issue on our GitHub.

Here test_Mafft_simple.py appears to be invoking mafft and
checking the teminal output to confirm it did something
sensible.

It appears there has been a subtle change in the terminal output.
We're looking for:

"Progressive alignment ..."

Instead there are lines:

"Progressive alignment 1/2..."

and:

"Progressive alignment 2/2..."

This looks like a simple change to use a regular expression,
or just search for "Progressive alignment".

Which version of mafft are you using?

Peter

On Wed, Sep 23, 2015 at 1:53 PM, Andreas Tille <andreas at an3as.eu> wrote:
> [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
>