[Biopython] BioPython unit tests: Mafft

[Peter Cock]

On Wed, Sep 23, 2015 at 3:24 PM, Andreas Tille <andreas at an3as.eu> wrote:
> Hi Peter,
>
> On Wed, Sep 23, 2015 at 02:50:03PM +0100, Peter Cock wrote:
>> 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.
>
> If you ask me to rather report via GitHub I might consider this next
> time.  This seems to be better than private e-mail.

Yes please for next time,

>> 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?
>
> ------------------------------------------------------------------------------
>   MAFFT v7.245 (2015/07/22)
>   http://mafft.cbrc.jp/alignment/software/
>   MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)
> ------------------------------------------------------------------------------
>

Working locally:

------------------------------------------------------------------------------
  MAFFT v6.717b (2009/12/03)
  http://align.bmr.kyushu-u.ac.jp/mafft/software/
  NAR 30:3059-3066 (2002), Briefings in Bioinformatics 9:286-298 (2008)
------------------------------------------------------------------------------

and:

------------------------------------------------------------------------------
  MAFFT v7.050b (2013/07/03)
  http://mafft.cbrc.jp/alignment/software/
  MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)
------------------------------------------------------------------------------

I can confirm updating to this version gave the same error:

------------------------------------------------------------------------------
  MAFFT v7.245 (2015/07/22)
  http://mafft.cbrc.jp/alignment/software/
  MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)
------------------------------------------------------------------------------

With this change it should work with either variant:

https://github.com/biopython/biopython/commit/dad073bc78109b926ea8de35f4140f9afc0953df

Or:

https://github.com/biopython/biopython/commit/dad073bc78109b926ea8de35f4140f9afc0953df.patch

Thanks,

Peter