[Bioperl-l] Announce: Bio::Seq::Quality

Heikki Lehvaslaiho heikki at ebi.ac.uk
Mon Jul 11 12:02:52 EDT 2005

Bio::Seq::Quality is a new module that allows you to store per-residue quality 
and trace index values using Bio::Seq::MetaI interface. It replaces 
Bio::Seq::SeqWithQuality which is now deprecated.

Solutions to persistence should focus on storing Bio::Seq::Meta and 
Bio::Seq::Meta::Array objects. It should be easy to stringify most real world 
meta values. Then the persistence could be implemented by storing the 
sequence object and N number of meta strings.

All the functional code is in Bio::Seq::Meta::Array, Bio::Seq::Quality merely 
adds a convenient interface.

The POD contains a discussion of differences from Bio::Seq::SeqWithQuality. 
If the following, or anything else,  is a problem let me know as soon as 

  The greatest difference to Bio::Seq::SeqWithQuality is that in this
  implementation quality for all sequence residues are automatically
  assigned a value of '0' (zero) unless you set it to something
  else. Length of the quality array always equals the length of the
  sequence. Therefore, length() never returns "DIFFERENT".


______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_ebi _ac _uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambridge, CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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