[BioRuby] test and bioruby shell questions

[Toshiaki Katayama]

Hi,

I also forgot to commit my change to ncbirest.rb for TogoWS (http://togows.dbcls.jp/).
I'll attach my current version (Apr 18) and I hope some of you can take a look on it.

Regards,
Toshiaki Katayama

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On 2008/10/14, at 1:05, Davide Rambaldi wrote:

>>
>>
>> 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])
>>
>
> I have modified to patch (see below), including a knowndbparams Hash.
>
> Now work with:
>
> bioruby> test = getobj("gb:AAF63163")
> bioruby> test = getobj("gp:AF237819")
>
>
> Actually the Hash handle genbank and genPept.
>
> How I can add more datatypes?
>
> I should take the definition in  NSIDs (lib/bio/io/dbget.rb) as key for knowdbparams Hash?
>
> Here is (from NCBI website) the list of available db params for efetch:
>
> 1. EFETCH for literature
>  db=[pubmed|pmc|journals|omim]
>
> 2. EFETCH for sequences
>  	? gene
> 	? genome
> 	? nucleotide
> 	? nuccore
> 	? nucest
> 	? nucgss
> 	? protein
> 	? popset
> 	? snp
> 	? sequences - Composite name including nucleotide, protein, popset and genome.
>
> 3. EFETCH for taxonomy
>  db=taxonomy
>
>
> Best Regards
>
> Davide
>
> -------------------------------------------------------
> PATCH HERE
> ----------------------------------------------------
>
> Oni:bioruby tucano$ git diff
> diff --git a/lib/bio.rb b/lib/bio.rb
> index b2b6f4f..bddc221 100644
> --- a/lib/bio.rb
> +++ b/lib/bio.rb
> @@ -170,6 +170,7 @@ module Bio
>
>  class NCBI
>    autoload :SOAP,       'bio/io/ncbisoap'
> +    autoload :REST,       'bio/io/ncbirest'
>  end
>
>
> diff --git a/lib/bio/shell/plugin/entry.rb b/lib/bio/shell/plugin/entry.rb
> index 6d36fb5..2408a95 100644
> --- a/lib/bio/shell/plugin/entry.rb
> +++ b/lib/bio/shell/plugin/entry.rb
> @@ -88,8 +88,19 @@ module Bio::Shell
>
>      # KEGG API at http://www.genome.jp/kegg/soap/
>      else
> -        puts "Retrieving entry from KEGG API (#{arg})"
>        entry = bget(arg)
> +        if entry.length != 0 then
> +          puts "Retrieving entry from KEGG API (#{arg})"
> +        else
> +          # NCBI efecth
> +          knowndbparams = {
> +            "gb" => {"db" => "sequences", "rettype" =>"gbwithparts"},
> +            "gp" => {"db" => "sequences", "rettype" => "gp"}
> +          }
> +          puts "Retrieving entry from NCBI (#{arg})"
> +          fetch = Bio::NCBI::REST.efetch(entry_id, knowndbparams[db])
> +          entry = fetch.to_s
> +        end
>      end
>    end
>
>
>
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