[Bioperl-l] BioPerl Physical Map modules, tests needed

Heikki Lehvaslaiho heikki at sanbi.ac.za
Mon Jan 23 02:54:02 EST 2006


Dear Gaurav,

I am going slowly through BioPerl modules that do not have any tests written 
to them. Unless there are tests in place, there is no way anyone can keep 
track of changes needed for the modules and useful modules will become 
obsolete as bioperl moves ahead.

You have contributed the following modules:

Bio::MapIO::fpc
Bio::Map::Clone
Bio::Map::Contig
Bio::Map::FPCMarker
Bio::Map::OrderedPositionWithDistance
Bio::Map::Physical

Would it be possible for you to write tests  and add them, together with  a 
small FPC sample file,  to the repository. I gave it a shot 
(t/PhysicalMap.t), but had to stop short when I realised that  
Bio::MapIO::fpc reads in an FPC file and creates a Bio::Map::Physical by 
holding everything in an internal hash. None of the objects included in a 
physical map are instantiated before they are required. It is therefore very 
difficult for someone else to write meaningful tests without a good example 
FPC file. 

Yours,
	-Heikki
-- 
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     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    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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