[BioRuby] test and bioruby shell questions

[Tomoaki NISHIYAMA]

Hi,

> - For the database I have used the general db "sequences", assuming  
> that the method getent of entry.rb is only for sequences... is this  
> correct?


There are getseq and getent:
My feeling is that both the databases and libraries are growing
to handles datatypes other than sequences,
though the sequences have been the primary interest.
So, I would assume getent might be used in more general purpose than  
getting "sequences".

I suppose that having a database with possible db parameter string and
remote db and rettype combination is a extensible way to resolve the  
need for possible different
datatypes.
knowndbparams={"gb" => {"db" => sequences, "rettype" =>"gbwithparts"},
  "gp" => {"db" => sequences, "rettype" => "gp"},
...
}

and call like
fetch = Bio::NCBI::REST.efetch(entry_id, knwondbparams[db])

Note that with "rettype" =>"gb", large scaffolds that are composed of
several different contigs are obtained as a list of the individual
contig and without the actual sequence. This is good for the response  
time,
and the network load when the sequence part is not necessary,
but sometimes unexpected for the user.  Until it becomes to possible
to fetch the underlying sequence upon the access to the sequence of the
entry, "gbwithparts" seems the parameter to use as default.
-- 
Tomoaki NISHIYAMA

Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan