bio 1.5.1 → 2.0.2

data/lib/bio/db/biosql/biosql_to_biosequence.rb

@@ -1,78 +0,0 @@
-#
-# = bio/db/biosql/biosql_to_biosequence.rb - Bio::SQL::Sequence to Bio::Sequence adapter module
-#
-# Copyright::   Copyright (C) 2008
-#               Naohisa Goto <ng@bioruby.org>,
-#               Raoul Jean Pierre Bonnal
-# License::     The Ruby License
-#
-# $Id:$
-#
-
-require 'bio/sequence'
-require 'bio/sequence/adapter'
-require 'bio/sequence/dblink'
-
-# Internal use only. Normal users should not use this module.
-#
-# Bio::SQL::Sequence to Bio::Sequence adapter module.
-# It is internally used in Bio::SQL::Sequence#to_biosequence.
-#
-module Bio::Sequence::Adapter::BioSQL
-
-  extend Bio::Sequence::Adapter
-
-  private
-
-  def_biosequence_adapter :seq 
-  
-  def_biosequence_adapter :entry_id
-
-  def_biosequence_adapter :primary_accession
-
-  def_biosequence_adapter :secondary_accessions
-
-  def_biosequence_adapter :molecule_type
-
-  #--
-  #TODO: identify where is stored data_class in biosql      
-  #++
-
-  def_biosequence_adapter :data_class
-
-  def_biosequence_adapter :definition, :description
-
-  def_biosequence_adapter :topology
-
-  def_biosequence_adapter :date_created
-
-  def_biosequence_adapter :date_modified
-  #do |bs|
-   #   Date.parse(bs.date_modified.to_s).strftime("%d-%b-%Y").upcase
-    # end
-
-  def_biosequence_adapter :division
-
-  def_biosequence_adapter :sequence_version
-
-  def_biosequence_adapter :keywords
-
-  def_biosequence_adapter :species
-
-  def_biosequence_adapter :classification, :taxonomy
-
-  def_biosequence_adapter :references
-
-  def_biosequence_adapter :features
-  
-  def_biosequence_adapter :comments
-
-  def_biosequence_adapter :other_seqids do |orig|
-    orig.identifier.split(',').collect do |dblink|
-      database, id = dblink.split(':')
-      Bio::Sequence::DBLink.new(database,id)
-    end
-  end
-
-end #module Bio::Sequence::Adapter::BioSQL
-

data/lib/bio/db/biosql/sequence.rb

@@ -1,444 +0,0 @@
-
-#TODO save on db reading from a genbank or embl object
-module Bio
-  class SQL
-
-
-
-    class Sequence
-      private
-      #      example
-      #      bioentry_qualifier_anchor :molecule_type, :synonym=>'mol_type'
-      #      this function creates other 3 functions, molecule_type, molecule_type=, molecule_type_update
-      #molecule_type => return an array of strings, where each string is the value associated with the qualifier, ordered by rank.
-      #molecule_type=value add a bioentry_qualifier value to the table
-      #molecule_type_update(value, rank) update an entry of the table with an existing rank
-      #the method inferr the qualifier term from the name of the first symbol, or you can specify a synonym to use
-
-      #creating an object with to_biosql is transaction safe.
-
-      #TODO: implement setting for more than a qualifier-vale.
-      def self.bioentry_qualifier_anchor(sym, *args)
-        options = args.first || Hash.new
-        #options.assert_valid_keys(:rank,:synonym,:multi)
-        method_reader = sym.to_s.to_sym
-        method_writer_operator = (sym.to_s+"=").to_sym
-        method_writer_modder = (sym.to_s+"_update").to_sym
-        synonym = options[:synonym].nil? ? sym.to_s : options[:synonym]
-
-        #DELETE        #Bio::SQL::Term.create(:name=>synonym, :ontology=> Bio::SQL::Ontology.find_by_name('Annotation Tags')) unless Bio::SQL::Term.exists?(:name =>synonym)
-        send :define_method, method_reader do
-          #return an array of bioentry_qualifier_values
-          begin
-            #DELETE            ontology_annotation_tags = Ontology.find_or_create({:name=>'Annotation Tags'})
-            term  = Term.first(:conditions=>["name = ?",synonym]) || Term.create({:name => synonym, :ontology=> Ontology.first(:conditions=>["name = ?",'Annotation Tags'])})
-            bioentry_qualifier_values = @entry.bioentry_qualifier_values.all(:conditions=>["term_id = ?",term.term_id])
-            data = bioentry_qualifier_values.map{|row| row.value} unless bioentry_qualifier_values.nil?
-            begin
-              # this block try to check if the data retrived is a
-              # Date or not and change it according to GenBank/EMBL format
-              # in that case return a string
-              # otherwise the []
-              Date.parse(data.to_s).strftime("%d-%b-%Y").upcase
-            rescue ArgumentError, TypeError, NoMethodError, NameError
-              data
-            end
-          rescue Exception => e
-            puts "Reader Error: #{synonym} #{e.message}"
-          end
-        end
-
-        send :define_method, method_writer_operator do |value|
-          begin
-            #DELETE            ontology_annotation_tags = Ontology.find_or_create({:name=>'Annotation Tags'})
-            term  = Term.first(:conditions=>["name = ?",synonym]) || Term.create({:name => synonym, :ontology=> Ontology.first(:conditions=>["name = ?",'Annotation Tags'])})
-            datas = @entry.bioentry_qualifier_values.all(:conditions=>["term_id = ?",term.term_id])
-            #add an element incrementing the rank or setting the first to 1
-            be_qu_va=@entry.bioentry_qualifier_values.build({:term=>term, :rank=>(datas.empty? ? 1 : datas.last.rank.succ), :value=>value})
-            be_qu_va.save
-          rescue Exception => e
-            puts "WriterOperator= Error: #{synonym} #{e.message}"
-          end
-        end
-
-        send :define_method, method_writer_modder do |value, rank|
-          begin
-            #DELETE            ontology_annotation_tags = Ontology.find_or_create({:name=>'Annotation Tags'})
-            term  = Term.first(:conditions=>["name = ?",synonym]) || Term.create({:name => synonym, :ontology=> Ontology.first(:conditions=>["name = ?",'Annotation Tags'])})
-            data = @entry.bioentry_qualifier_values.all(:term_id=>term.term_id, :rank=>rank)
-            if data.nil?
-              send method_writer_operator, value
-            else
-              data.value=value
-              data.save
-            end
-          rescue Exception => e
-            puts "WriterModder Error: #{synonym} #{e.message}"
-          end
-        end
-
-      end
-
-      public
-      attr_reader :entry
-
-      def delete
-        #TODO: check is references connected to this bioentry are leaf or not.
-        #actually I think it should be more sofisticated, check if there are
-        #other bioentries connected to references; if not delete 'em
-        @entry.references.each { |ref| ref.delete if ref.bioentries.size==1}
-        @entry.destroy
-      end
-
-      def get_seqfeature(sf)
-
-        #in seqfeature BioSQL class
-        locations_str = sf.locations.map{|loc| loc.to_s}.join(',')
-        #pp sf.locations.inspect
-        locations_str = "join(#{locations_str})" if sf.locations.count>1
-        Bio::Feature.new(sf.type_term.name, locations_str,sf.seqfeature_qualifier_values.collect{|sfqv| Bio::Feature::Qualifier.new(sfqv.term.name,sfqv.value)})
-      end
-
-      def length=(len)
-        @entry.biosequence.length=len
-      end
-
-      def initialize(options={})
-        #options.assert_valid_keys(:entry, :biodatabase,:biosequence)
-        return @entry = options[:entry] unless options[:entry].nil?
-
-        return to_biosql(options[:biosequence], options[:biodatabase]) unless options[:biosequence].nil? or options[:biodatabase].nil?
-
-      end
-
-      def to_biosql(bs,biodatabase)
-        #DELETE        #Transcaction works greatly!!!
-        begin
-          #DELETE          Bioentry.transaction do
-          @entry = biodatabase.bioentries.build({:name=>bs.entry_id})
-
-          puts "primary" if $DEBUG
-          self.primary_accession = bs.primary_accession
-
-          puts "def" if $DEBUG
-          self.definition = bs.definition unless bs.definition.nil?
-
-          puts "seqver" if $DEBUG
-          self.sequence_version = bs.sequence_version || 0
-
-          puts "divi" if $DEBUG
-          self.division = bs.division unless bs.division.nil?
-
-          puts "identifier" if $DEBUG
-          self.identifier = bs.other_seqids.collect{|dblink| "#{dblink.database}:#{dblink.id}"}.join(';') unless bs.other_seqids.nil?
-          @entry.save
-          puts "secacc" if $DEBUG
-
-          bs.secondary_accessions.each do |sa|
-            puts "#{sa}" if $DEBUG
-            #write as qualifier every secondary accession into the array
-            self.secondary_accessions = sa
-          end unless bs.secondary_accessions.nil?
-
-
-          #to create the sequence entry needs to exists
-          puts "seq" if $DEBUG
-          puts bs.seq if $DEBUG
-          self.seq = bs.seq unless bs.seq.nil?
-          puts "mol" if $DEBUG
-
-          self.molecule_type = bs.molecule_type unless bs.molecule_type.nil?
-          puts "dc" if $DEBUG
-
-          self.data_class = bs.data_class unless bs.data_class.nil?
-          puts "top" if $DEBUG
-          self.topology = bs.topology unless bs.topology.nil?
-          puts "datec" if $DEBUG
-          self.date_created = bs.date_created unless bs.date_created.nil?
-          puts "datemod" if $DEBUG
-          self.date_modified = bs.date_modified unless bs.date_modified.nil?
-          puts "key" if $DEBUG
-
-          bs.keywords.each do |kw|
-            #write as qualifier every secondary accessions into the array
-            self.keywords = kw
-          end unless bs.keywords.nil?
-
-          puts "spec" if $DEBUG
-          #self.species = bs.species unless bs.species.nil?
-          self.species = bs.species unless bs.species.empty?
-          puts "Debug: #{bs.species}" if $DEBUG
-          puts "Debug: feat..start" if $DEBUG
-
-          bs.features.each do |feat|
-            self.feature=feat
-          end unless bs.features.nil?
-
-          puts "Debug: feat...end" if $DEBUG
-          bs.references.each do |reference|
-            self.reference=reference
-          end unless bs.references.nil?
-
-          bs.comments.each do |comment|
-            self.comment=comment
-          end unless bs.comments.nil?
-
-          #DELETE          end #transaction
-          return self
-        rescue Exception => e
-          puts "to_biosql exception: #{e}"
-          puts $!
-        end #rescue
-      end #to_biosql
-
-
-      def name
-        @entry.name
-      end
-      alias entry_id name
-
-      def name=(value)
-        @entry.name=value
-      end
-      alias entry_id= name=
-
-      def primary_accession
-        @entry.accession
-      end
-
-      def primary_accession=(value)
-        @entry.accession=value
-      end
-
-      #TODO      def secondary_accession
-      #        @entry.bioentry_qualifier_values
-      #      end
-
-      def organism
-        @entry.taxon.nil? ? "" : "#{@entry.taxon.taxon_scientific_name.name}"+ (@entry.taxon.taxon_genbank_common_name ? "(#{@entry.taxon.taxon_genbank_common_name.name})" : '')
-      end
-      alias species organism
-
-      def organism=(value)
-        #FIX there is a shortcut
-        taxon_name=TaxonName.first(:conditions=>["name = ? and name_class = ?",value.gsub(/\s+\(.+\)/,''),'scientific name'])
-        if taxon_name.nil?
-          puts "Error value doesn't exists in taxon_name table with scientific name constraint."
-        else
-          @entry.taxon_id=taxon_name.taxon_id
-          @entry.save
-        end
-      end
-      alias species= organism=
-
-      def database
-        @entry.biodatabase.name
-      end
-
-      def database_desc
-        @entry.biodatabase.description
-      end
-
-      def version
-        @entry.version
-      end
-      alias sequence_version version
-
-      def version=(value)
-        @entry.version=value
-      end
-      alias sequence_version= version=
-
-      def division
-        @entry.division
-      end
-
-      def division=(value)
-        @entry.division=value
-      end
-
-      def description
-        @entry.description
-      end
-      alias definition description
-
-      def description=(value)
-        @entry.description=value
-      end
-      alias definition= description=
-
-      def identifier
-        @entry.identifier
-      end
-      alias other_seqids identifier
-
-      def identifier=(value)
-        @entry.identifier=value
-      end
-
-      bioentry_qualifier_anchor :data_class
-      bioentry_qualifier_anchor :molecule_type, :synonym=>'mol_type'
-      bioentry_qualifier_anchor :topology
-      bioentry_qualifier_anchor :date_created
-      bioentry_qualifier_anchor :date_modified, :synonym=>'date_changed'
-      bioentry_qualifier_anchor :keywords, :synonym=>'keyword'
-      bioentry_qualifier_anchor :secondary_accessions, :synonym=>'secondary_accession'
-
-      def features
-        @entry.seqfeatures.collect do |sf|
-          self.get_seqfeature(sf)
-        end
-      end
-
-      def feature=(feat)
-        #ToDo: avoid Ontology find here, probably more efficient create class variables
-        #DELETE        type_term_ontology = Ontology.find_or_create({:name=>'SeqFeature Keys'})
-        puts "feature:type_term = #{feat.feature}" if $DEBUG
-        type_term = Term.first(:conditions=>["name = ?", feat.feature]) || Term.create({:name=>feat.feature, :ontology=>Ontology.first(:conditions=>["name = ?",'SeqFeature Keys'])})
-        #DELETE        source_term_ontology = Ontology.find_or_create({:name=>'SeqFeature Sources'})
-        puts "feature:source_term" if $DEBUG
-        source_term = Term.first(:conditions=>["name = ?",'EMBLGenBankSwit'])
-        puts "feature:seqfeature" if $DEBUG
-        seqfeature = @entry.seqfeatures.build({:source_term=>source_term, :type_term=>type_term, :rank=>@entry.seqfeatures.count.succ, :display_name=>''})
-        seqfeature.save
-        puts "feature:location" if $DEBUG
-        feat.locations.each do |loc|
-          location = seqfeature.locations.build({:seqfeature=>seqfeature, :start_pos=>loc.from, :end_pos=>loc.to, :strand=>loc.strand, :rank=>seqfeature.locations.count.succ})
-          location.save
-        end
-
-        #DELETE        qual_term_ontology = Ontology.find_or_create({:name=>'Annotation Tags'})
-
-        puts "feature:qualifier" if $DEBUG
-        feat.each do |qualifier|
-          #DELETE          qual_term = Term.find_or_create({:name=>qualifier.qualifier}, {:ontology=>qual_term_ontology})
-          qual_term = Term.first(:conditions=>["name = ?", qualifier.qualifier]) || Term.create({:name=>qualifier.qualifier, :ontology=>Ontology.first(:conditions=>["name = ?", 'Annotation Tags'])})
-          qual = seqfeature.seqfeature_qualifier_values.build({:seqfeature=>seqfeature, :term=>qual_term, :value=>qualifier.value.to_s, :rank=>seqfeature.seqfeature_qualifier_values.count.succ})
-          qual.save
-
-        end
-      end
-
-      #return the seqfeature mapped from BioSQL with a type_term like 'CDS'
-      def cdsfeatures
-        @entry.cdsfeatures
-      end
-
-      # Returns the sequence.
-      # Returns a Bio::Sequence::Generic object.
-
-      def seq
-        s = @entry.biosequence
-        Bio::Sequence::Generic.new(s ? s.seq : '')
-      end
-
-      def seq=(value)
-        #TODO: revise this piece of code.
-        #chk which type of alphabet is, NU/NA/nil
-        if @entry.biosequence.nil?
-          #DELETE          puts "intoseq1"
-          @entry.biosequence = Biosequence.new(:seq=>value)
-          #          biosequence = @entry.biosequence.build({:seq=>value})
-          @entry.biosequence.save
-          #          biosequence.save
-        else
-          @entry.biosequence.seq=value
-        end
-        self.length=value.length
-        #DELETE        #@entry.biosequence.length=value.length
-        #DELETE        #break
-        @entry.save
-      end
-
-      #report parents and exclude info with "no rank". Now I report rank == class but ... Question ? Have to be reported taxonomy with rank=="class"?
-      def taxonomy
-        tax = []
-        taxon = Taxon.first(:conditions=>["taxon_id = ?",@entry.taxon.parent_taxon_id])
-        while taxon and taxon.taxon_id != taxon.parent_taxon_id and taxon.node_rank!='no rank'
-          tax << taxon.taxon_scientific_name.name if taxon.node_rank!='class'
-          #Note: I don't like this call very much, correct with a relationship in the ref class.
-          taxon = Taxon.first(:conditions=>["taxon_id = ?",taxon.parent_taxon_id])
-        end
-        tax.reverse
-      end
-
-      def length
-        @entry.biosequence.length
-      end
-
-      def references
-        #return and array of hash, hash has these keys ["title", "dbxref_id", "reference_id", "authors", "crc", "location"]
-        #probably would be better to d a class refrence to collect these informations
-        @entry.bioentry_references.collect do |bio_ref|
-          hash = Hash.new
-          hash['authors'] = bio_ref.reference.authors.gsub(/\.\s/, "\.\s\|").split(/\|/) if (bio_ref.reference and bio_ref.reference.authors)
-
-          hash['sequence_position'] = "#{bio_ref.start_pos}-#{bio_ref.end_pos}" if (bio_ref.start_pos and bio_ref.end_pos)
-          hash['title'] = bio_ref.reference.title
-          hash['embl_gb_record_number'] = bio_ref.rank
-          #TODO: solve the problem with specific comment per reference.
-          #TODO: get dbxref
-          #take a look when location is build up in def reference=(value)
-
-          bio_ref.reference.location.split('|').each do |element|
-            key,value=element.split('=')
-            hash[key]=value
-          end unless bio_ref.reference.location.nil?
-
-          hash['xrefs'] = bio_ref.reference.dbxref ? "#{bio_ref.reference.dbxref.dbname}; #{bio_ref.reference.dbxref.accession}." : ''
-          Bio::Reference.new(hash)
-        end
-      end
-
-      def comments
-        @entry.comments.map do |comment|
-          comment.comment_text
-        end
-      end
-
-      def reference=(value)       
-        locations=Array.new
-        locations << "journal=#{value.journal}" unless value.journal.empty?
-        locations << "volume=#{value.volume}" unless value.volume.empty?
-        locations << "issue=#{value.issue}" unless value.issue.empty?
-        locations << "pages=#{value.pages}" unless value.pages.empty?
-        locations << "year=#{value.year}" unless value.year.empty?
-        locations << "pubmed=#{value.pubmed}" unless value.pubmed.empty?
-        locations << "medline=#{value.medline}" unless value.medline.empty?
-        locations << "doi=#{value.doi}" unless value.doi.nil?
-        locations << "abstract=#{value.abstract}" unless value.abstract.empty?
-        locations << "url=#{value.url}" unless value.url.nil?
-        locations << "mesh=#{value.mesh}" unless value.mesh.empty?
-        locations << "affiliations=#{value.affiliations}" unless value.affiliations.empty?
-        locations << "comments=#{value.comments.join('~')}"unless value.comments.nil?
-        start_pos, end_pos = value.sequence_position ? value.sequence_position.gsub(/\s*/,'').split('-') : [nil,nil]
-        reference= Reference.first(:conditions=>["title = ?",value.title]) || Reference.create({:title=>value.title,:authors=>value.authors.join(' '), :location=>locations.join('|')})
-        bio_reference=@entry.bioentry_references.build({:reference=>reference,:rank=>value.embl_gb_record_number, :start_pos=>start_pos, :end_pos=>end_pos})
-        bio_reference.save
-      end
-
-      def comment=(value)
-        #DELETE        comment=Comment.new({:bioentry=>@entry, :comment_text=>value, :rank=>@entry.comments.count.succ})
-        comment = @entry.comments.build({:comment_text=>value, :rank=>@entry.comments.count.succ})
-        comment.save
-      end
-
-      def save
-        #I should add chks for SQL errors
-        @entry.biosequence.save
-        @entry.save
-      end
-      def to_fasta
-        ">" + accession + "\n" + seq.gsub(Regexp.new(".{1,#{60}}"), "\\0\n")
-      end
-
-      def to_fasta_reverse_complememt
-        ">" + accession + "\n" + seq.reverse_complement.gsub(Regexp.new(".{1,#{60}}"), "\\0\n")
-      end
-
-      def to_biosequence
-        Bio::Sequence.adapter(self,Bio::Sequence::Adapter::BioSQL)
-      end
-    end #Sequence
-  end #SQL
-end #Bio