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

Chris Fields cjfields at illinois.edu
Mon Jan 4 22:54:03 EST 2010


Jean-Marc,

You can do that, yes.  Just curious, but have you looked at the various flat file indexing modules for FASTA?  Bio::DB::Fasta and Bio::Index::Fasta are commonly used and allow lookups by primary ID (and I think in some cases secondary IDs).

chris

On Jan 4, 2010, at 8:12 AM, Jean-Marc Frigerio INRA wrote:

> ...
> 
> Hi,
> 
> I wrote and currently use a module I named Bio::SeqIO::multifasta, which is basically a copy of Bio::SeqIO::fasta plus a few methods:
> get_by_id(), get_by_order(), first_seq() and previous_seq()
> 
> It would need review, validation etc. Do I submit it to Bugzilla ?
> 
> 	-- jmf
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