wwood-bioruby 1.2.11

data/lib/bio/db/url.rb

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+module Bio
+  # A module dedicated to providing URLs to common bioinformatic databases.
+  module URLGenerators
+    def pantherdb_panther_family_url(panther_id)
+      "http://www.pantherdb.org/panther/family.do?clsAccession=#{panther_id}"
+    end
+     
+    def hhmi_pfam_family_url(pfam_family_id)
+      "http://pfam.janelia.org/family?entry=#{pfam_family_id}&type=Family"
+    end
+     
+    def plasmodb_gene_url(plasmodb_id)
+      "http://plasmodb.org/gene/#{plasmodb_id}"
+    end
+    
+    def pdb_url(pdbId)
+      "http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=#{pdbId}"
+    end
+   
+    def pdbsum_url(pdbId)
+      "http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=#{pdbId}"
+    end
+   
+    def cath_url(pdbId)
+      "http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/SearchPdb.pl?query=#{pdbId}&type=PDB"
+    end
+   
+    def scop_url(pdbId)
+      "http://scop.mrc-lmb.cam.ac.uk/scop/pdb.cgi?disp=scop&id=#{pdbId}"
+    end
+  end
+  
+  # Convenience class that allows easier creation of URLs.
+  # Use case: I have a gene name (PF11_0344) and I want to be able to generate
+  # a link to the corresponding PlasmoDB gene page, I can call Bio::URL.plasmodb_gene_url('PF11_0344')
+  class URL
+    # Include all the URL generators as static methods
+    class << self
+      include URLGenerators
+    end
+  end
+end

data/lib/bio/feature.rb

@@ -0,0 +1,139 @@
+#
+# = bio/feature.rb - Features/Feature class (GenBank Feature table)
+#
+# Copyright::	Copyright (c) 2002, 2005  Toshiaki Katayama <k@bioruby.org>
+#                             2006        Jan Aerts <jan.aerts@bbsrc.ac.uk>
+# License::	The Ruby License
+#
+# $Id: feature.rb,v 1.13.2.1 2008/03/04 10:12:22 ngoto Exp $
+
+require 'bio/location'
+
+module Bio
+
+# = DESCRIPTION
+# Container for the sequence annotation.
+#
+# = USAGE
+#  # Create a Bio::Feature object.
+#  # For example: the GenBank-formatted entry in genbank for accession M33388
+#  # contains the following feature:
+#  #    exon     1532..1799
+#  #             /gene="CYP2D6"
+#  #             /note="cytochrome P450 IID6; GOO-132-127"
+#  #             /number="1"
+#  feature = Bio::Feature.new('exon','1532..1799')
+#  feature.append(Bio::Feature::Qualifier.new('gene', 'CYP2D6'))
+#  feature.append(Bio::Feature::Qualifier.new('note', 'cytochrome P450 IID6'))
+#  feature.append(Bio::Feature::Qualifier.new('number', '1'))
+#
+#  # or all in one go:
+#  feature2 = Bio::Feature.new('exon','1532..1799',
+#    [ Bio::Feature::Qualifier.new('gene', 'CYP2D6'),
+#      Bio::Feature::Qualifier.new('note', 'cytochrome P450 IID6; GOO-132-127'),
+#      Bio::Feature::Qualifier.new('number', '1')
+#    ])
+#
+#  # Print the feature
+#  puts feature.feature + "\t" + feature.position
+#  feature.each do |qualifier|
+#    puts "- " + qualifier.qualifier + ": " + qualifier.value
+#  end
+#
+# = REFERENCES
+# INSD feature table definition:: http://www.ddbj.nig.ac.jp/FT/full_index.html
+class Feature
+  # Create a new Bio::Feature object.
+  # *Arguments*:
+  # * (required) _feature_: type of feature (e.g. "exon")
+  # * (required) _position_: position of feature (e.g. "complement(1532..1799)")
+  # * (opt) _qualifiers_: list of Bio::Feature::Qualifier objects (default: [])
+  # *Returns*:: Bio::Feature object
+  def initialize(feature = '', position = '', qualifiers = [])
+    @feature, @position, @qualifiers = feature, position, qualifiers
+  end
+
+  # Returns type of feature in String (e.g 'CDS', 'gene')
+  attr_accessor :feature
+
+  # Returns position of the feature in String (e.g. 'complement(123..146)')
+  attr_accessor :position
+
+  # Returns an Array of Qualifier objects.
+  attr_accessor :qualifiers
+
+  # Returns a Bio::Locations object translated from the position string.
+  def locations
+    Locations.new(@position)
+  end
+
+  # Appends a Qualifier object to the Feature.
+  # 
+  # *Arguments*:
+  # * (required) _qualifier_: Bio::Feature::Qualifier object
+  # *Returns*:: Bio::Feature object
+  def append(a)
+    @qualifiers.push(a) if a.is_a? Qualifier
+    return self
+  end
+
+  # Iterates on each qualifier object.
+  #
+  # *Arguments*:
+  # * (optional) _key_: if specified, only iterates over qualifiers with this key
+  def each(arg = nil)
+    @qualifiers.each do |x|
+      next if arg and x.qualifier != arg
+      yield x
+    end
+  end
+
+  # Returns a Hash constructed from qualifier objects.
+  def assoc
+    STDERR.puts "Bio::Feature#assoc is deprecated, use Bio::Feature#to_hash instead" if $DEBUG
+    hash = Hash.new
+    @qualifiers.each do |x|
+      hash[x.qualifier] = x.value
+    end
+    return hash
+  end
+
+  # Returns a Hash constructed from qualifier objects.
+  def to_hash
+    hash = Hash.new
+    @qualifiers.each do |x|
+      hash[x.qualifier] ||= []
+      hash[x.qualifier] << x.value
+    end
+    return hash
+  end
+
+  # Short cut for the Bio::Feature#to_hash[key]
+  def [](key)
+    self.to_hash[key]
+  end
+
+  # Container for qualifier-value pairs for sequence features.
+  class Qualifier
+    # Creates a new Bio::Feature::Qualifier object
+    #
+    # *Arguments*:
+    # * (required) _key_: key of the qualifier (e.g. "gene")
+    # * (required) _value_: value of the qualifier (e.g. "CYP2D6")
+    # *Returns*:: Bio::Feature::Qualifier object
+    def initialize(key, value)
+      @qualifier, @value = key, value
+    end
+
+    # Qualifier name in String
+    attr_reader :qualifier
+
+    # Qualifier value in String
+    attr_reader :value
+
+  end #Qualifier
+
+end #Feature
+
+end # Bio
+

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

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+module Bio
+		class SQL
+			class Biodatabase < DummyBase
+				has_many :bioentries, :class_name =>"Bioentry", :foreign_key => "biodatabase_id"
+				validates_uniqueness_of :name
+			end
+		end #SQL
+end #Bio	
+
+
+if __FILE__ == $0
+  require 'rubygems'
+  require 'composite_primary_keys'
+  require 'bio'
+  require 'pp'
+  
+  #  pp connection = Bio::SQL.establish_connection('bio/io/biosql/config/database.yml','development')
+  pp connection = Bio::SQL.establish_connection({'test'=>{'database'=>"bio_test", 'adapter'=>"postgresql", 'username'=>"rails", 'password'=>nil}},'test')
+  #pp YAML::load(ERB.new(IO.read('bio/io/biosql/config/database.yml')).result)
+  if true
+    pp Bio::SQL.list_entries
+
+    puts "### GenBank"
+    if ARGV.size > 0
+	gb = Bio::GenBank.new(ARGF.read)
+    else
+	require 'bio/io/fetch'
+	gb = Bio::GenBank.new(Bio::Fetch.query('gb', 'AJ224122'))
+    end
+
+   	biosequence = gb.to_biosequence
+	db=Bio::SQL::Biodatabase.new(:biodatabase_id=>3,:name=>"JEFF", :authority=>"ME", :description=>"YOU")
+	db.save!
+	
+	#sqlseq = Bio::SQL::Sequence.new(:biosequence=>biosequence,:biodatabase_id=>db.id)
+
+	#    bioseq = Bio::SQL.fetch_accession('AJ224122')   
+	#    pp bioseq
+	#    pp bioseq.entry_id    
+    #TODO create a test only for tables not sequence here
+#    pp bioseq.molecule_type
+    #pp  bioseq.molecule_type.class
+    #bioseq.molecule_type_update('dna', 1)
+    pp Bio::SQL::Taxon.find(8121).taxon_names
+    
+	    #sqlseq.to_biosequence
+	
+	#sqlseq.delete
+  end
+  #pp  bioseq.molecule_type
+  #term = Bio::SQL::Term.find_by_name('mol_type')
+  #pp term
+  #pp bioseq.entry.bioentry_qualifier_values.create(:term=>term, :rank=>2, :value=>'pippo')
+  #pp bioseq.entry.bioentry_qualifier_values.inspect
+  #pp bioseq.entry.bioentry_qualifier_values.find_all_by_term_id(26)
+  #pp primo.class
+  #  pp primo.value='dna'
+  #  pp primo.save
+  #pp bioseq.molecule_type= 'prova'
+  
+  #Bio::SQL::BioentryQualifierValue.delete(delete.bioentry_id,delete.term_id,delete.rank)
+  
+  
+end

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

@@ -0,0 +1,29 @@
+module Bio
+    class SQL
+			class Bioentry < DummyBase
+				belongs_to :biodatabase, :class_name => "Biodatabase"
+				belongs_to :taxon, :class_name => "Taxon"
+				has_one :biosequence
+				#, :class_name => "Biosequence", :foreign_key => "bioentry_id"
+				has_many :comments, :class_name =>"Comment", :order =>'rank'
+				has_many :seqfeatures, :class_name => "Seqfeature", :order=>'rank'
+				has_many :bioentry_references, :class_name=>"BioentryReference" #, :foreign_key => "bioentry_id"
+				has_many :bioentry_dbxrefs, :class_name => "BioentryDbxref"
+				has_many :object_bioentry_relationships, :class_name=>"BioentryRelationship", :foreign_key=>"object_bioentry_id" #non mi convince molto credo non funzioni nel modo corretto
+				has_many :subject_bioentry_relationships, :class_name=>"BioentryRelationship", :foreign_key=>"subject_bioentry_id" #non mi convince molto credo non funzioni nel modo corretto
+
+				has_many :cdsfeatures, :class_name=>"Seqfeature", :foreign_key =>"bioentry_id", :conditions=>["term.name='CDS'"], :include=>"type_term"
+        
+        has_many :terms, :through=>:bioentry_qualifier_values, :class_name => "Term"
+        #NOTE: added order_by for multiple hit and manage ranks correctly
+        has_many :bioentry_qualifier_values, :order=>"bioentry_id,term_id,rank", :class_name => "BioentryQualifierValue"
+        
+				#per la creazione richiesti:
+				#name, accession, version
+#				validates_uniqueness_of :accession, :scope=>[:biodatabase_id]
+#				validates_uniqueness_of :name, :scope=>[:biodatabase_id] 
+			#	validates_uniqueness_of :identifier, :scope=>[:biodatabase_id]
+				
+			end
+		end #SQL
+end #Bio

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

@@ -0,0 +1,11 @@
+module Bio
+		class SQL
+			class BioentryDbxref < DummyBase
+#delete				set_sequence_name nil
+				set_primary_key nil #bioentry_id,dbxref_id
+				belongs_to :bioentry, :class_name => "Bioentry"
+				belongs_to :dbxref, :class_name => "Dbxref"
+			end
+    		end #SQL
+end #Bio	
+

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

@@ -0,0 +1,12 @@
+module Bio
+    class SQL
+			class BioentryPath < DummyBase
+				set_primary_key nil
+#delete				set_sequence_name nil
+				belongs_to :term, :class_name => "Term"
+				#da sistemare per poter procedere.
+				belongs_to :object_bioentry, :class_name=>"Bioentry"
+				belongs_to :subject_bioentry, :class_name=>"Bioentry"
+			end #BioentryPath
+		end #SQL
+end #Bio

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
+