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

[Ewan Birney]

On Fri, 2 Feb 2001, Hilmar Lapp wrote:

> "J. Schaefer" wrote:
> > 
> > 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.
> > 
> > Am I just missing something?  Or should I just write a temporary file and
> > slurp it in with SeqIO:Seq?
> > 
> 

No. I think you are looking for the Bio::Seq constructor, like

   $seq = Bio::Seq->new( -seq=> 'ATGGGGTGGGTTTATGGGG' , -id => 'id');

right?

If you have a file as an array of lines from a file there is a perl module
to make it  "look like" a file... (? IO::String....?)


> I'm not sure I understand your question. There is no SeqIO::Seq class.
> Would you like to emulate a sequence stream (Bio::SeqIO compliant
> object) from an array of sequence objects? If so, is there a
> particular reason that you can't pass on the array of seq objects to
> the method which would otherwise receive the sequence stream?
> 
> 	Hilmar
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp@gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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