[Bioperl-l] Bio::SeqIO::FTHelper

Heikki Lehvaslaiho heikki at sanbi.ac.za
Fri Mar 2 01:08:15 EST 2007


This sounds great. Is the speed increase noticeable?

	-Heikki


On Thursday 01 March 2007 17:24:03 Chris Fields wrote:
> I do have a rough outline of what I think could be done:
>
> http://www.bioperl.org/wiki/Handler-based_SeqIO_parsers
>
> where you could switch out handlers to deal with incoming data
> chunks.  Any suggestions there are welcome.
>
> I'll probably commit examples of the above in the next week or two
> (GenBank, EMBL, Swiss parsers using the same handlers) which don't
> use FTHelper.  So far I have all three passing tests based on genbank/
> embl/swiss.t but they need a few more tweaks before I commit.
>
> chris
>
> On Mar 1, 2007, at 5:02 AM, Heikki Lehvaslaiho wrote:
> > Chris,
> >
> > It was meant to collect code that was common to all three main
> > databases using
> > similar feature tables.
> >
> > Now might be the time to optimise the parsing speed by removing it.
> > Do you
> > have a plan how to do it?
> >
> > 	-Heikki
> >
> > On Tuesday 27 February 2007 22:57:40 Chris Fields wrote:
> >> Could anyone tell me what FTHelper is used for?  From what I gather
> >> it rolls up seqfeature data into a lightweight object but then
> >> creates a SeqFeature::Generic anyway (at least for GenBank/EMBL/
> >> Swiss), which seems to be a waste of memory and time.  Is there
> >> something I'm missing (besides my sanity of course)?
> >>
> >> chris
> >> _______________________________________________
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> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > --
> > ______ _/      _/_____________________________________________________
> >       _/      _/
> >      _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
> >     _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
> >    _/  _/  _/  SANBI, South African National Bioinformatics Institute
> >   _/  _/  _/  University of Western Cape, South Africa
> >      _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
> > ___ _/_/_/_/_/________________________________________________________
> > _______________________________________________
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>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign



-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
___ _/_/_/_/_/________________________________________________________


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