[Bioperl-l] How to read in the whole fasta file in the memory?
Jason Stajich
jason at bioperl.org
Mon Jan 4 16:03:45 UTC 2010
We typically think of SeqIO as parsing a stream of data, not being
reliant on it being a file which is what these methods would be
implying I think. Sounds a lot like a database - does Bio::DB::Fasta
not provide some of the functionality you need by these methods? I
realize there isn't a by_order() but the get_by_id() is implemented to
allow random access.
-jason
>
> 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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--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
http://fungalgenomes.org/
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