[Bioperl-l] Bio::Tools::BPlite

[Ewan Birney]

On Sat, 15 Jul 2000, Lorenz Pollak wrote:

> > There is a massive advantage here, as alot of the systems in
> 
> Nice to hear! :-)
> 
> > Bio::Seq/Bio::SeqIO rely on things inherieting from Bio::SeqFeatureI - you
> > should also set primary_tag and source_tag to sensible values.
> 
> for the query feature:
> primary_tag = "blast_query"
> source_tag = $report->query (ac, id or name supplied with the query)
> 
> for the sbjct feature:
> primary_tag = "blast_sbjct"
> source = $sbjct->name (ac, id, name of sbjct)


No. This are too specific. The $report->query should go in the seqname
field and the $sbjct->name into the seqname field of the hit on the other
side.

For both features it should be

   primary_tag - similarity
   source_tag  - BLAST



 > 
> how about these?
> 
> > Have you added a BPLite specific test?
> 
> I will do that in the next days.
> (along with adding docs and some minor 
> enhancements like using hashed constructors 
> in all three modules)
> 
> kind regards,
> Lorenz
>