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

Heikki Lehvaslaiho heikki at ebi.ac.uk
Wed Jul 13 10:49:09 EDT 2005

I've been cleaning Bio::Seq::SeqWithQuality usage from bioperl-live modules 
and replacing it with Bio::Seq::Quality. Everything seems to work.

I've left Bio::Seq::PrimaryQual for the next rewrite. Its functionality is all 
in the Quality class (get and set id and quality values), but you can not get 
the quality values from a Bio::Seq::Quality object if you do not have the 
sequence set. Usually qualities without residues do not make such sense, but 
there is something in Bio::Assembly code or at least in its tests that need 
plain qualities.


On Monday 11 July 2005 17:02, Heikki Lehvaslaiho wrote:
> 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
> possible:
>   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".
> Enjoy,
>  -Heikki

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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_ebi _ac _uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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  _/  _/  _/  Cambridge, CB10 1SD, United Kingdom
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