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