[Bioperl-l] How to read in the whole fasta file in the memory?

[Mark A. Jensen]

I think you might want Bio::AlignIO:

$alnio = Bio::AlignIO->new(-file=> 'my.fas' );
$aln = $alnio->next_aln;
@seqs = $aln->each_seqs;

MAJ
----- Original Message ----- 
From: "Peng Yu" <pengyu.ut at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Wednesday, December 30, 2009 12:26 PM
Subject: [Bioperl-l] How to read in the whole fasta file in the memory?


> With Bio::SeqIO, I can only read in the records in a fasta file one by
> one. This is preferable if there are many records in a file.
> 
> But I also want to read all the records in. I could use a while loop
> to read all records in. But could somebody let me know if there is a
> function in bioperl that can read in all the record at once and return
> me an object?
> 
> http://www.bioperl.org/wiki/HOWTO:SeqIO
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