[Bioperl-l] tcoffee tests in BioPerl

[Heikki Lehvaslaiho]

The %identity of alignments are identical in Jason's older t_Coffee
program. This confirms that sequence order in t_coffee alignements
differs between program versions.

I'll write more robust tests.

	-Heikki


Heikki Lehvaslaiho wrote:
> 
> Peter and Jason,
> 
> cc: Cedric
> 
> To really start using Bio::SimpleAlign, I installed clustalw (v. 1.81)
> and TCoffee (v. 1.34).  No problems there; tests provided with the
> programs pass. All the clustalw bioperl tests passed (after I fixed
> the nse names), too.
> 
> TCoffee bioperl tests, however, complain even after I've changed the
> expected nse to "id/start-end":
> 
> 1..13
> ok 1
> ok 2
> ok 3
> ok 4
> ok 5
> ok 6
> not ok 7
> # Test 7 got: 'CATH_HUMAN/1-335' (t/TCoffee.t at line 86)
> #   Expected: 'CATL_HUMAN/1-333'
>     ( failed tcoffee profile alignment using input file
> CATH_HUMAN/1-335)
> not ok 8
> # Test 8 got: 'CATH_HUMAN/1-335' (t/TCoffee.t at line 97)
> #   Expected: 'CATL_HUMAN/1-333'
>     (failed tcoffee profile alignment using SimpleAlign input
> CATH_HUMAN/1-335)
> ok 9
> ok 10
> ok 11
> ok 12
> not ok 13
> # Test 13 got: 'CATH_HUMAN/1-335' (t/TCoffee.t at line 113)
> #    Expected: 'CATH_RAT/1-333'
>      (failed adding new sequence to alignment CATH_HUMAN/1-335)
> 
> Tests 9..12 are new and show that the new sequence really get inserted
> into the alignment. By printing out data structures, I've verified
> that profile alingments work, too.
> 
> It seems to me  that since version 1.34 is most probably newer than
> versions used when the  test were created, the way TCoffee orders
> sequences in the alignment might have changed. In fact, I did not find
> from the program documentation anything that would make me expect that
> the output sequences should be in any particular order. I'll cc: this
> mail to Cedric to get his comment on this.
> 
> If only the order has changed, the percentage_identity() of the
> alignment should be the same even in older versions. Tests 10 and 12
> give the integer values 41 and 47 before and after adding the new
> sequence.
> 
> Jason/Peter, could you do 'cvs update' and see if these %identity
> values hold even with the t_coffee versions you are using?
> 
> I ran the clustalw and tcoffee tests under bioperl-07 which I have not
> updated and got identical results. It was a relief to find get an
> extra confirmation that I have not messed up anything in the bioperl
> alignment code.
> 
> If everything is as I suspect, it is easy enough change the tests from
> checking a name of the sequence in a given position in the alignment
> (which conflict the data encapsulation principle!) to comparing the
> number sequences in the alignment.
> 
>         -Heikki
> 
> --
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________