bio 1.2.1 → 1.3.0

data/lib/bio/io/biosql/bioentry_qualifier_value.rb

@@ -0,0 +1,10 @@
+module Bio
+  class SQL
+    class BioentryQualifierValue < DummyBase
+      #NOTE: added rank to primary_keys, now it's finished.
+      set_primary_keys :bioentry_id, :term_id, :rank
+      belongs_to :bioentry, :class_name => "Bioentry"
+      belongs_to :term, :class_name => "Term"
+    end #BioentryQualifierValue
+  end #SQL
+end #Bio

data/lib/bio/io/biosql/bioentry_reference.rb

@@ -0,0 +1,10 @@
+module Bio
+    class SQL
+			class BioentryReference < DummyBase
+				set_primary_keys :bioentry_id, :reference_id, :rank
+				belongs_to :bioentry, :class_name => "Bioentry"
+				belongs_to :reference , :class_name => "Reference"
+			end		
+		end #SQL
+end #Bio		
+

data/lib/bio/io/biosql/bioentry_relationship.rb

@@ -0,0 +1,10 @@
+module Bio
+    class SQL
+			class BioentryRelationship < DummyBase
+#delete				set_primary_key "bioentry_relationship_id"
+				set_sequence_name "bieontry_relationship_pk_seq"
+				belongs_to :object_bioentry, :class_name => "Bioentry"
+				belongs_to :subject_bioentry, :class_name => "Bioentry"
+			end
+		end #SQL
+end #Bio		    

data/lib/bio/io/biosql/biosequence.rb

@@ -0,0 +1,11 @@
+module Bio
+    class SQL
+			class Biosequence < DummyBase
+				set_primary_key "bioentry_id"
+#delete				set_sequence_name "biosequence_pk_seq"
+				belongs_to :bioentry, :foreign_key=>"bioentry_id"
+				#has_one :bioentry
+				#, :class_name => "Bioentry"
+			end
+		end #SQL
+end #Bio		   

data/lib/bio/io/biosql/comment.rb

@@ -0,0 +1,7 @@
+ module Bio
+    class SQL
+			class Comment < DummyBase
+			      belongs_to :bioentry, :class_name => "Bioentry"
+			end
+		end #SQL
+end #Bio		   

data/lib/bio/io/biosql/config/database.yml

@@ -0,0 +1,20 @@
+#This is the database configuration specific for BioSQL
+#User can configure it's db here
+
+development:
+  adapter: postgresql
+  database: biorails_development
+  username: rails
+  password: 
+
+test:
+  adapter: postgresql
+  database: biorails_test
+  username: rails
+  password: 
+  
+production:
+  adapter: postgresql
+  database: biorails_production
+  username: rails
+  password: 

data/lib/bio/io/biosql/dbxref.rb

@@ -0,0 +1,13 @@
+ module Bio
+    class SQL
+			class Dbxref < DummyBase
+			      #set_sequence_name "dbxref_pk_seq"
+			      has_many :dbxref_qualifier_values, :class_name => "DbxrefQualifierValue"
+			      has_many :locations, :class_name => "Location"
+			      has_many :references, :class_name=>"Reference"
+			      has_many :term_dbxrefs, :class_name => "TermDbxref"
+			      has_many :bioentry_dbxrefs, :class_name => "BioentryDbxref"
+            #TODO: check is with bioentry there is an has_and_belongs_to_many relationship has specified in schema overview.
+			    end
+    		end #SQL
+end #Bio		

data/lib/bio/io/biosql/dbxref_qualifier_value.rb

@@ -0,0 +1,12 @@
+ module Bio
+    class SQL
+			class DbxrefQualifierValue < DummyBase
+				#think to use composite primary key
+			      set_primary_key nil #dbxref_id, term_id, rank
+#delete			      set_sequence_name nil
+			      belongs_to :dbxref, :class_name => "Dbxref"
+			      belongs_to :term, :class_name => "Term"
+			    end		
+		end #SQL
+end #Bio		
+

data/lib/bio/io/biosql/location.rb

@@ -0,0 +1,32 @@
+module Bio
+  class SQL 
+    class Location < DummyBase
+      #set_sequence_name "location_pk_seq"
+      belongs_to :seqfeature, :class_name => "Seqfeature"
+      belongs_to :dbxref, :class_name => "Dbxref"
+      belongs_to :term, :class_name => "Term"
+      has_many :location_qualifier_values, :class_name => "LocationQualifierValue"
+      
+      def to_s
+        if strand==-1
+          str="complement("+start_pos.to_s+".."+end_pos.to_s+")"
+        else
+          str=start_pos.to_s+".."+end_pos.to_s
+        end
+        return str    
+      end
+      
+      def sequence
+        seq=""
+        unless self.seqfeature.bioentry.biosequence.seq.nil?
+          seq=Bio::Sequence::NA.new(self.seqfeature.bioentry.biosequence.seq[start_pos-1..end_pos-1])
+          seq.reverse_complement! if strand==-1
+        end
+        return seq        
+      end
+      
+      
+      
+    end
+  end #SQL
+end #Bio

data/lib/bio/io/biosql/location_qualifier_value.rb

@@ -0,0 +1,11 @@
+ module Bio
+    class SQL 
+			class LocationQualifierValue <  DummyBase
+			      set_primary_key nil #location_id, term_id
+#delete			      set_sequence_name nil
+			      belongs_to :location, :class_name => "Location"
+			      belongs_to :term, :class_name => "Term"
+			    end		
+		end #SQL
+end #Bio
+

data/lib/bio/io/biosql/ontology.rb

@@ -0,0 +1,10 @@
+
+ module Bio
+    class SQL 
+		    class Ontology < DummyBase
+		      has_many :terms, :class_name => "Term"
+		      has_many :term_paths, :class_name => "TermPath"
+		      has_many :term_relationships, :class_name => "TermRelationship"
+		    end		
+		end #SQL
+end #Bio

data/lib/bio/io/biosql/reference.rb

@@ -0,0 +1,9 @@
+
+ module Bio
+    class SQL 
+		    class Reference < DummyBase  
+		      belongs_to :dbxref, :class_name => "Dbxref"
+		      has_many :bioentry_references, :class_name=>"BioentryRefernce"
+		    end		
+		end #SQL
+end #Bio

data/lib/bio/io/biosql/seqfeature.rb

@@ -0,0 +1,32 @@
+
+module Bio
+  class SQL 
+    class Seqfeature <DummyBase  
+      set_sequence_name "seqfeature_pk_seq"
+      belongs_to :bioentry
+      #, :class_name => "Bioentry"
+      belongs_to :type_term, :class_name => "Term", :foreign_key => "type_term_id"
+      belongs_to :source_term, :class_name => "Term", :foreign_key =>"source_term_id"
+      has_many :seqfeature_dbxrefs, :class_name => "SeqfeatureDbxref", :foreign_key => "seqfeature_id"
+      has_many :seqfeature_qualifier_values, :order=>'rank', :foreign_key => "seqfeature_id"
+      #, :class_name => "SeqfeatureQualifierValue"
+      has_many :locations, :class_name => "Location", :order=>'rank'
+      has_many :object_seqfeature_paths, :class_name => "SeqfeaturePath", :foreign_key => "object_seqfeature_id"
+      has_many :subject_seqfeature_paths, :class_name => "SeqfeaturePath", :foreign_key => "subject_seqfeature_id"
+      has_many :object_seqfeature_relationships, :class_name => "SeqfeatureRelationship", :foreign_key => "object_seqfeature_id"
+      has_many :subject_seqfeature_relationships, :class_name => "SeqfeatureRelationship", :foreign_key => "subject_seqfeature_id"
+
+      #get the subsequence described by the locations objects
+      def sequence
+        return self.locations.inject(Bio::Sequence::NA.new("")){|seq, location| seq<<location.sequence}
+    end
+    
+      #translate the subsequences represented by the feature and its locations
+      #not considering the qualifiers 
+      #Return a Bio::Sequence::AA object
+      def translate(*args)
+        self.sequence.translate(*args)
+      end
+      end		
+    end #SQL
+  end #Bio

data/lib/bio/io/biosql/seqfeature_dbxref.rb

@@ -0,0 +1,11 @@
+
+ module Bio
+    class SQL 
+		    class SeqfeatureDbxref < DummyBase
+		      set_primary_keys :seqfeature_id, :dbxref_id
+#delete		      set_sequence_name nil
+		      belongs_to :seqfeature, :class_name => "Seqfeature", :foreign_key => "seqfeature_id"
+		      belongs_to :dbxref, :class_name => "Dbxref", :foreign_key => "dbxref_id"
+		    end		
+		end #SQL
+end #Bio

data/lib/bio/io/biosql/seqfeature_path.rb

@@ -0,0 +1,11 @@
+ module Bio
+    class SQL 
+			   class SeqfeaturePath < DummyBase
+			      set_primary_keys :object_seqfeature_id, :subject_seqfeature_id, :term_id
+			      set_sequence_name nil
+			      belongs_to :object_seqfeature, :class_name => "Seqfeature", :foreign_key => "object_seqfeature_id"
+			      belongs_to :subject_seqfeature, :class_name => "Seqfeature", :foreign_key => "subject_seqfeature_id"
+            belongs_to :term, :class_name => "Term"
+			    end		
+		end #SQL
+end #Bio

data/lib/bio/io/biosql/seqfeature_qualifier_value.rb

@@ -0,0 +1,20 @@
+
+module Bio
+  class SQL 
+    class SeqfeatureQualifierValue < DummyBase
+      set_primary_keys  :seqfeature_id, :term_id, :rank
+      set_sequence_name nil
+      belongs_to :seqfeature
+      belongs_to :term, :class_name => "Term"
+      
+      def self.find_cluster(query)
+        term_note= Term.find_by_name('note')
+        find(:all, :conditions =>["value like ? and term_id = ?", "cl:#{query}", term_note])
+      end
+      def self.find_cluster_info(query)
+        term_note= Term.find_by_name('note')
+        find(:all, :conditions =>["value like ? and term_id = ?", "cli:#{query}", term_note])
+      end
+    end		
+  end #SQL
+end #Bio

data/lib/bio/io/biosql/seqfeature_relationship.rb

@@ -0,0 +1,11 @@
+
+ module Bio
+    class SQL 
+			    class SeqfeatureRelationship <DummyBase
+			      set_sequence_name "seqfeatue_relationship_pk_seq"
+			      belongs_to :term, :class_name => "Term"
+			      belongs_to :object_seqfeature, :class_name => "Seqfeature"
+			      belongs_to :subject_seqfeature, :class_name => "Seqfeature"
+			    end		
+		end #SQL
+end #Bio

data/lib/bio/io/biosql/taxon.rb

@@ -0,0 +1,12 @@
+
+ module Bio
+    class SQL 
+			    class Taxon < DummyBase
+			      set_sequence_name "taxon_pk_seq"
+			      has_many :taxon_names, :class_name => "TaxonName"
+		              has_one :taxon_scientific_name, :class_name => "TaxonName", :conditions=>"name_class = 'scientific name'"
+		              has_one :taxon_genbank_common_name, :class_name => "TaxonName", :conditions=>"name_class = 'genbank common name'"
+			      has_one :bioentry, :class_name => "Bioentry"
+			    end		
+		end #SQL
+end #Bio

data/lib/bio/io/biosql/taxon_name.rb

@@ -0,0 +1,9 @@
+
+ module Bio
+    class SQL 
+			    class TaxonName < DummyBase
+			      set_primary_keys :taxon_id, :name, :name_class
+			      belongs_to :taxon, :class_name => "Taxon"      
+			    end		
+		end #SQL
+end #Bio

data/lib/bio/io/biosql/term.rb

@@ -0,0 +1,27 @@
+
+ module Bio
+    class SQL 
+			    class Term < DummyBase
+			      belongs_to :ontology, :class_name => "Ontology"
+			      has_many :seqfeature_qualifier_values, :class_name => "SeqfeatureQualifierValue"
+			      has_many :dbxref_qualifier_values, :class_name => "DbxrefQualifierValue"
+            has_many :bioentry_qualifer_values, :class_name => "BioentryQualifierValue"
+            has_many :bioentries, :through=>:bioentry_qualifier_values
+			      has_many :locations, :class_name => "Location"
+			      has_many :seqfeature_relationships, :class_name => "SeqfeatureRelationship"
+			      has_many :term_dbxrefs, :class_name => "TermDbxref"
+			      has_many :term_relationship_terms, :class_name => "TermRelationshipTerm"
+			      has_many :term_synonyms, :class_name => "TermSynonym"
+			      has_many :location_qualifier_values, :class_name => "LocationQualifierValue"
+			      has_many :seqfeature_types, :class_name => "Seqfeature", :foreign_key => "type_term_id"			      
+			      has_many :seqfeature_sources, :class_name => "Seqfeature", :foreign_key => "source_term_id"			      
+			      has_many :term_path_subjects, :class_name => "TermPath", :foreign_key => "subject_term_id"
+			      has_many :term_path_predicates, :class_name => "TermPath", :foreign_key => "predicate_term_id"
+			      has_many :term_path_objects, :class_name => "TermPath", :foreign_key => "object_term_id"			      
+			      has_many :term_relationship_subjects, :class_name => "TermRelationship", :foreign_key =>"subject_term_id"
+			      has_many :term_relationship_predicates, :class_name => "TermRelationship", :foreign_key =>"predicate_term_id"
+			      has_many :term_relationship_objects, :class_name => "TermRelationship", :foreign_key =>"object_term_id"
+            has_many :seqfeature_paths, :class_name => "SeqfeaturePath"
+			    end		
+		end #SQL
+end #Bio

data/lib/bio/io/biosql/term_dbxref.rb

@@ -0,0 +1,11 @@
+
+ module Bio
+    class SQL 
+			    class TermDbxref < DummyBase
+			      set_primary_key nil #term_id, dbxref_id
+#delete			      set_sequence_name nil
+			      belongs_to :term, :class_name => "Term"
+			      belongs_to :dbxref, :class_name => "Dbxref"
+			    end		
+		end #SQL
+end #Bio

data/lib/bio/io/biosql/term_path.rb

@@ -0,0 +1,12 @@
+
+ module Bio
+    class SQL 
+			    class TermPath < DummyBase
+			      set_sequence_name "term_path_pk_seq"
+			      belongs_to :ontology, :class_name => "Ontology"
+			      belongs_to :subject_term, :class_name => "Term"
+			      belongs_to :object_term, :class_name => "Term"
+			      belongs_to :predicate_term, :class_name => "Term"
+			    end		
+		end #SQL
+end #Bio

data/lib/bio/io/biosql/term_relationship.rb

@@ -0,0 +1,13 @@
+
+ module Bio
+    class SQL 
+			    class TermRelationship < DummyBase
+			      set_sequence_name "term_relationship_pk_seq"
+			      belongs_to :ontology, :class_name => "Ontology"
+			      belongs_to :subject_term, :class_name => "Term"
+			      belongs_to :predicate_term, :class_name => "Term"
+			      belongs_to :object_term, :class_name => "Term"
+			      has_one :term_relationship_term, :class_name => "TermRelationshipTerm"
+			    end		
+		end #SQL
+end #Bio

data/lib/bio/io/biosql/term_relationship_term.rb

@@ -0,0 +1,11 @@
+
+ module Bio
+    class SQL 
+			    class TermRelationshipTerm < DummyBase
+#delete			      set_sequence_name nil
+			      set_primary_key :term_relationship_id
+			      belongs_to :term_relationship, :class_name => "TermRelationship"
+			      belongs_to :term, :class_name => "Term"
+			    end		
+		end #SQL
+end #Bio

data/lib/bio/io/biosql/term_synonym.rb

@@ -0,0 +1,10 @@
+
+ module Bio
+    class SQL 
+			    class TermSynonym < DummyBase
+#delete			      set_sequence_name nil
+			      set_primary_key nil
+			      belongs_to :term, :class_name => "Term"
+			    end		
+		end #SQL
+end #Bio

data/lib/bio/io/das.rb

@@ -6,7 +6,7 @@
 #		Toshiaki Katayama <k@bioruby.org>
 # License::	The Ruby License
 #
-# $Id: das.rb,v 1.17 2007/07/16 18:06:12 k Exp $
+# $Id:$
 #
 #--
 # == TODO
@@ -47,7 +47,7 @@ class DAS
   # Returns an Array of Bio::DAS::DSN
   def get_dsn
     ary = []
-    result, = Bio::Command.post_form("#{@server}/das/dsn")
+    result = Bio::Command.post_form("#{@server}/das/dsn")
     doc = REXML::Document.new(result.body)
     doc.elements.each('/descendant::DSN') do |e|
       dsn = DSN.new
@@ -78,7 +78,7 @@ class DAS
     else
       src = dsn
     end
-    result, = Bio::Command.post_form("#{@server}/das/#{src}/entry_points")
+    result = Bio::Command.post_form("#{@server}/das/#{src}/entry_points")
     doc = REXML::Document.new(result.body)
     doc.elements.each('/descendant::ENTRY_POINTS') do |e|
       entry_point.href = e.attributes['href']
@@ -112,7 +112,7 @@ class DAS
       opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
     end
 
-    result, = Bio::Command.post_form("#{@server}/das/#{dsn}/dna", opts)
+    result = Bio::Command.post_form("#{@server}/das/#{dsn}/dna", opts)
     doc = REXML::Document.new(result.body)
     doc.elements.each('/descendant::SEQUENCE') do |e|
       sequence = DNA.new
@@ -144,7 +144,7 @@ class DAS
       opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
     end
 
-    result, = Bio::Command.post_form("#{@server}/das/#{dsn}/sequence", opts)
+    result = Bio::Command.post_form("#{@server}/das/#{dsn}/sequence", opts)
     doc = REXML::Document.new(result.body)
     doc.elements.each('/descendant::SEQUENCE') do |e|
       sequence = SEQUENCE.new
@@ -181,7 +181,7 @@ class DAS
       opts << "segment=#{s.entry_id}:#{s.start},#{s.stop}"
     end
 
-    result, = Bio::Command.post_form("#{@server}/das/#{dsn}/types", opts)
+    result = Bio::Command.post_form("#{@server}/das/#{dsn}/types", opts)
     doc = REXML::Document.new(result.body)
     doc.elements.each('/descendant::GFF') do |e|
       types.version = e.attributes['version']
@@ -232,7 +232,7 @@ class DAS
       opts << "group_id=#{gid}"
     end
 
-    result, = Bio::Command.post_form("#{@server}/das/#{dsn}/features", opts)
+    result = Bio::Command.post_form("#{@server}/das/#{dsn}/features", opts)
     doc = REXML::Document.new(result.body)
     doc.elements.each('/descendant::GFF') do |e|
       gff.version = e.attributes['version']