update TogoWS documentation. genbank -> ncbi-nucleotide

bioruby · Oct 18, 2018 · d71e07a · d71e07a
1 parent 02a9642
commit d71e07a
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/lib/bio/io/togows.rb b/lib/bio/io/togows.rb
@@ -107,14 +107,14 @@ def reset_togows_access_wait
     # 
     # For light users, class methods can be used.
     #
-    #   print Bio::TogoWS::REST.entry('genbank', 'AF237819')
+    #   print Bio::TogoWS::REST.entry('ncbi-nucleotide', 'AF237819')
     #   print Bio::TogoWS::REST.search('uniprot', 'lung cancer')
     #
     # For heavy users, an instance of the REST class can be created, and
     # using the instance is more efficient than using class methods.
     #
     #   t = Bio::TogoWS::REST.new
-    #   print t.entry('genbank', 'AF237819')
+    #   print t.entry('ncbi-nucleotide', 'AF237819')
     #   print t.search('uniprot', 'lung cancer')
     #
     # == References
@@ -222,9 +222,9 @@ def retrieve(ids, hash = {})
       #
       # Example:
       #   t = Bio::TogoWS::REST.new
-      #   kuma = t.entry('genbank', 'AF237819')
+      #   kuma = t.entry('ncbi-nucleotide', 'AF237819')
       #   # multiple IDs at a time
-      #   misc = t.entry('genbank', [ 'AF237819', 'AF237820' ])
+      #   misc = t.entry('ncbi-nucleotide', [ 'AF237819', 'AF237820' ])
       #   # with format change
       #   p53 = t.entry('uniprot', 'P53_HUMAN', 'fasta')
       #
@@ -366,7 +366,7 @@ def self.search_database_list(*arg)
       # Access to the TogoWS by using GET method.
       #
       # Example 1:
-      #   get('entry', 'genbank', AF209156')
+      #   get('entry', 'ncbi-nucleotide', AF209156')
       # Example 2:
       #   get('search', 'uniprot', 'lung cancer')
       #

diff --git a/sample/test_restriction_enzyme_long.rb b/sample/test_restriction_enzyme_long.rb
@@ -14,7 +14,7 @@
 require 'benchmark'
 require 'bio'
 
-entry = Bio::TogoWS::REST.entry('genbank', 'BA000007.2')
+entry = Bio::TogoWS::REST.entry('ncbi-nucleotide', 'BA000007.2')
 EcoliO157H7Seq = Bio::GenBank.new(entry).naseq.freeze
 
 module TestRestrictionEnzymeAnalysisCutLong