[Bioperl-l] Announce: Bio::Seq::Quality
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
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
> 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".
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_/ _/ _/ Heikki Lehvaslaiho heikki at_ebi _ac _uk
_/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute
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_/ _/ _/ Cambridge, CB10 1SD, United Kingdom
_/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468
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