[Bioperl-l] seqIO

[Desmond Lim]

Hi Lincoln,

Thanks but what am I to do after this?

I have a file that contains EMBL sequences. And I'm reading it into an array, manipulating it and then print it a file in fasta format.

I know how to use the:

my $seq_in = Bio::SeqIO->new('-file' => filename1, '-format' => 'embl');
my $seq_out = Bio::SeqIO->new('-file' => filename2, '-format' => 'fasta'); 

while ( my $inseq = $seq_in->next_seq ) {
  $seq_out->write_seq($inseq);
}

But I don't have a file for filename1 but an array. Is there a way for reading the array (the manipulated embl one) and then write it as a fasta file?

Thanks.

-----Original Message-----
From: Lincoln Stein [mailto:lstein at cshl.edu]
Sent: Wednesday, October 08, 2003 7:18 AM
To: Desmond Lim; Hilmar Lapp; BioPerl
Subject: Re: [Bioperl-l] seqIO


If you have an array of sequences then you can just create them using 
Bio::Seq:

	@bioperl_sequences = map {Bio::Seq->new(-seq=>$_)} @raw_seq;

Lincoln


On Tuesday 07 October 2003 12:45 am, Desmond Lim wrote:
> > What made you think it would accept a -ph parameter? Besides, if
> > there was
> > one you'd have to provide an array reference.
>
> I didn't think it would work but I wanted to try it out.
>
> What I'm trying to do is get SeqIO to accept an array of sequences and not
> a file.
>
> Desmond
>
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-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
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