[Bioperl-l] Re: MicroarrayIO proposal

[Ewan Birney]

Steve - Allen and Adam --

This discussion seems to be me bang on about the design, the relationship
to MAGE-ML and the consistency to bioperl - Allen - I know you are the
driver here (do... keep driving. Bioperl needs Drivers!) but I think the
ideas from Steve and Adam are really good to listen into.


Steve - I guess your internal classes to Affy data are probably quite
mature and not relevant to move across into this.


I suspect the naive interface of:

  # pseudo code, doesn't work, probably not the right tags for
  # formats

  $exp_in = Bio::ExpressionIO->new( -format => 'affy' , -file =>
"myfile.affy");
 
  $exp_out = Bio::ExpressionIO->new( -format => 'mage-ml' , -file =>
">out.mage");

  $expt = $exp_in->next_experiment();

  # perhaps we need to add some stuff to be MAGE ML compliant
  $expt->experiment_type( Bio::Ontology::Factory->new( -short_name =>
'miami_experiment')->('cancer_comparison') );
  $expt->submitter('birney@ebi.ac.uk');

  # write it out

  $exp_out->write_experiment($expt);




Would be ideal. Obviously $expt would also have accessor methods for the
Features etc






-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------