[Bioperl-l] Bio::Tools::Run::Mdust

[Heikki Lehvaslaiho]

Hi Donald,

I started using your Mdust module in bioperl-run and run into problems 
immediately.

* Only Bio::Seq objects are accepted but not Bio::PrimarySeq objects,
  although the docs say otherwise
* Sequences are modified in place. That is really bad, because that 
  means that the user has to know to create a copy before 
  running Mdust on it.
* The docs say that you have to set MDUSTDIR envvar to tell the program 
  where to find the binary. That is actually optional if the 
  binary is on your path.
* The tests do not cover any of the options to the program


As a quick fix, I suggest that we:

* leave the current way of working for Bio::SeqI objects:
  sequence string is not masked but seqfeatures to that effect are added
* Modify run() to return the new masked sequence object when 
  the target is a Bio::PrimarySeqI.
* fix the documentation


After that it will be possible to simply write:

use Bio::Tools::Run::Mdust;
$mdust = Bio::Tools::Run::Mdust->new();
$seq_dusted = $m->run($seq); # $seq->isa(PrimarySeqI);


Are you happy for me to do this or do you want to do it yourself?


Yours,
	-Heikki

-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    
    _/_/_/_/_/  heikki at_sanbi _ac _za    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
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