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

Jason Stajich jason at bioperl.org
Mon Jan 4 11:03:45 EST 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
http://fungalgenomes.org/



More information about the Bioperl-l mailing list