[BioRuby] A question for BioRuby newbies

[Pjotr Prins]

Hi Mic,

On Thu, Feb 09, 2012 at 08:38:08AM +1000, Mic wrote:
>    * a gff3 support which doesn't read the whole file in the memory
>    see [1]http://biopython.org/wiki/GFF_Parsing#Limiting_to_features_of_interest

The current bio-gff3 biogem only loads an index into memory, which is
not too costly, and caches records. The problem with the GFF3 standard
is (potentially) deep references, which is not so relevant for 99% of
real GFF3 data. I agree we can do better. Still, for most practical
purposes, the bio-gff3-plugin gem delivers. You may want to use the 

  lru,line,lazy      75m      75m      0m17 (0.8.6) 50K   730M
 
version. See the explanation on

  https://github.com/pjotrp/bioruby-gff3-plugin

It is a tad slow. About six times slower than the full memory version.

Speed is the first improvement I would work on.

Pj.