Bioperl: Reading from a stream into Bio::Seq
Tue, 27 Oct 1998 17:05:05 +0000 (GMT)
On Tue, 27 Oct 1998, Lincoln Stein wrote:
> If this is a general problem, I'd recommend that we work on an XML or
> Boulder-like syntax for serializing Bio::* objects. An easy, but
> Perl-specific, alternative is simply to use the Perl Data::Dumper
> serialization class.
I think serialization of objects should be a 'good thing' and a possible
candidate for inclusion into the Bio::Root stuff - though I don't want
to see Bio::Root becoming a monster 'blob' object.
We would be *alot* better off if we could have some higher level language/
documentation control about precisely what fields were in the objects.
(hohohohoho...OOP perl...makes you laugh sometimes).
*BUT* that's not what I wanted. I want to get things out of SRS v.easily.
(one day... srs will properely compile into perl...). So the stream would
be in fasta format.
Both would be nice. ;)
> James Gilbert writes:
> > I'd like to be able to make a new Seq object from
> > a fromatted string (or array) as well as from a
> > stream.
> > On Thu, 22 Oct 1998, Ewan Birney wrote:
> > >
> > > I should really know this, but does anyone know whether you can
> > > construct a Bio::Seq from a stream (eg, opened via a pipe from getz)
> > > rather than a filename?
> > >
> > > If not... i should put this in ;)
> > James G.R. Gilbert
> > The Sanger Centre
> > Wellcome Trust Genome Campus
> > Hinxton
> > Cambridge Tel: 01223 494906
> > CB10 1SA Fax: 01223 494919
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> > ====================================================================
> Lincoln D. Stein Cold Spring Harbor Laboratory
> firstname.lastname@example.org Cold Spring Harbor, NY
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