[BioRuby] test and bioruby shell questions
Davide Rambaldi
davide.rambaldi at ifom-ieo-campus.it
Sun Oct 12 15:10:14 UTC 2008
Il giorno 26/set/08, alle ore 15:37, Naohisa GOTO ha scritto:
> Thank you for a patch, but it has some problems:
> For KEGG API, $?.exitstatus has no mean, and no need to check $?.
> The "AF237819" should not be hardcoded because the method is
> not only for demo, but a bioruby-shell command to fetch entry
> specified by a user. Also note that "db" => "nuccore" would
> not always be good. (If result is empty, switching to another
> database and trying again would be the best way.)
I apologize for this.... was really stupid and sorry for the late
answer (my laptop have died... with all my bioruby test inside)
Maybe I can propose anther patch: the patch to bio.rb add an autoload
call for Bio::NCBI::REST in bio.rb, the patch to bio/shell/plugin/
entry.rb don't have the entry hardcoded.
About the entry.rb patch I have two questions:
- I put the db prefix (demo is gb:AF237819) to define the rettype for
NCBI::REST. Work for the demo. but I guess this should be changed...
- 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?
PATCHES:
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..21ef9f6 100644
--- a/lib/bio/shell/plugin/entry.rb
+++ b/lib/bio/shell/plugin/entry.rb
@@ -88,8 +88,14 @@ 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
+ puts "Retrieving entry from NCBI (#{arg})"
+ fetch = Bio::NCBI::REST.efetch(entry_id,
{"db"=>"sequences", "rettype"=>db})
+ entry = fetch.to_s
+ end
end
end
Best Regards.
Davide Rambaldi,
Bioinformatics PhD student.
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