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

Hilmar Lapp lapp@gnf.org
Fri, 02 Feb 2001 11:46:58 -0800

"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?

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 Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757