Bioperl: Reading from a stream into Bio::Seq

[Ewan Birney]

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. ;)



> 
> Lincoln
> 
> 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
> lstein@cshl.org			                  Cold Spring Harbor, NY
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Ewan Birney
<birney@sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/

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