[Bioperl-l] Bio::Index::Fasta vs Bio::DB::Fasta

[Lincoln Stein]

Hi Folks,

I've just recently become aware that Bio::Index::Fasta has very heavy 
overlapping functionality with Bio::DB::Fasta, and this is likely to lead to 
some user confusion down the road.

I would remove Bio::DB::Fasta in favor of the Bio::Index version, except that 
I don't think that Bio::Index::Fasta does the thing that first motivated 
Bio::DB::Fasta, which was the ability to retrieve subsequences efficiently.  
I have big (tens of megabyte) fasta files that contain 
whole C. elegans chromosomes, and want to fetch a few base pairs from the 
middle of them without reading the whole record into memory.  Can 
Bio::Index::Fasta do this?

Lincoln

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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