[Bioperl-l] avoiding temporary files

[Jason Stajich]

no then you need to use the parser
my $io = new IO::String($seqstring);
my $seqio = new Bio::SeqIO(-format => 'embl', -fh => $io);

This is how we pull data off the web with LWP in the Bio::DB modules that
retrieve from a remote site and get the whole record in a string.

On Wed, 17 Apr 2002, Matthew Pocock wrote:

> Does this work if $seqstring is a complete EMBL entry?
>
> Matthew
>
> Jason Stajich wrote:
> > See the Bio::PrimarySeq or Bio::Seq perldoc man pages
> > (online at docs.bioperl.org)
> >
> > my $seqstring = 'CAGTGTA';
> > my $seq = new Bio::Seq(-seq => $seqstring,
> > 		       -display_id => 'IDNUMBER',
> > 		       -desc => 'a description might go here');
> >
> >
> > On Wed, 17 Apr 2002, Stephen Baird wrote:
> >
> >
> >>Hi,
> >>  I think this is a basic perl question but I can't figure it out and
> >>since it is with my bioperl calls I'm sure one of you will know the
> >>answer.  I would like to take a sequence file that is in a single variable
> >>like from a textarea of a webpage and make it into a sequence object
> >>without writing it to a temporary file.  It would be nice for me to do
> >>this with any program that I call through perl....like blastall where the
> >>query sequence does not have to be written as temporary file.
> >>
> >>Is this possible?
> >>
> >>Thanks,
> >>
> >>Stephen Baird
> >>Molecular Genetics
> >>Children's Hospital of Eastern Ontario
> >>401 Smyth Rd.
> >>Ottawa, Ontario
> >>Canada
> >>K1H 8L1
> >>
> >>tel: 613-738-3925
> >>fax: 613-738-4833
> >>
> >>
> >>_______________________________________________
> >>Bioperl-l mailing list
> >>Bioperl-l@bioperl.org
> >>http://bioperl.org/mailman/listinfo/bioperl-l
> >>
> >
> >
>
>
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu