[Bioperl-l] seqIO

[Hilmar Lapp]

On 10/6/03 7:43 PM, "Desmond Lim" <btclimd at nus.edu.sg> wrote:

> Hi,
> 
> I'm trying to make an array into a SeqIO object
> 
> my $seq_in = Bio::SeqIO->new('-ph' => @arr, '-format' => 'fasta');
> 

What made you think it would accept a -ph parameter? Besides, if there was
one you'd have to provide an array reference.

> but it doesn't work. I have gone through the documentation for the SeqIO
> module but have no idea how to 'read' the sequences directly from an array.
> 
> I need to do this because there is a sequence manipulation that happens to the
> file that is opened in the beginning.
> 

I'm not sure I understand your use case. Could you try to elaborate a bit.

If what you're attempting to do is apply post-processing to the sequences
coming off of a sequence file through a SeqIO module and have the result
appear as a SeqIO-compatible stream to pass on, Bio::Seq::BaseSeqProcessor
may be for you (that's what it was designed for).

    -hilmar


> I have a work around of creating a file with the array and then opening it
> using -file but I think reading from an array should be possible.
> 
> Thanks.
> 
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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