[Bioperl-l] SeqIO: input from memory not file

[J. Schaefer]

Thanks much!  I had missed that part of the perldoc.  I appreciate the
help of the list.

Jonathan

---------------------------------------------------------------
Jonathan B. Schaefer

Beavo Lab			University of Washington
Box 357280, Room K363		Molecular and Cellular Biology Program
1959 NE Pacific St.             v:(206)221-4585
Seattle, WA 98195-7280		f:(206)685-3822
							

On Fri, 2 Feb 2001, Jason Stajich wrote:

> 
> ----- Original Message -----
> From: "J. Schaefer" <schaefer@u.washington.edu>
> To: <bioperl-l@bioperl.org>
> Sent: Friday, February 02, 2001 2:16 PM
> Subject: [Bioperl-l] SeqIO: input from memory not file
> 
> 
> > Hi-
> >
> > I'm just getting into bioperl and have found a limitation which I
> > haven't been able navigate around.
> >
> > I would like to create a series of SeqIO:Seq objects directly from an
> > array of sequence references.  The constructors for SeqIO:Seq only allow
> > new objects to be made from files, filehandles or STDIN.
> >
> > I am able to make a PrimarySeq object directly from memory, but I can't
> > see how to convert a PrimarySeq into a SeqIO:Seq.
> 
> It's easier than that. If you want to make a seq you would do
> my $seq = new Bio::Seq(-seq => 'AAGCGAGAGAGAG',
>                                             -moltype=>'dna', -id =>
> 'myseq1');
> 
> See the documentation for Bio::Seq (perldoc Bio::Seq)
> 
> >
> > Am I just missing something?  Or should I just write a temporary file and
> > slurp it in with SeqIO:Seq?
> >
> > Thanks for your feedback,
> >
> > Jonathan
> >
> > ---------------------------------------------------------------
> > Jonathan B. Schaefer
> >
> > Beavo Lab University of Washington
> > Box 357280, Room K363 Molecular and Cellular Biology Program
> > 1959 NE Pacific St.             v:(206)221-4585
> > Seattle, WA 98195-7280 f:(206)685-3822
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>