bio 0.7.0

data/lib/bio/io/soapwsdl.rb

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+#
+# = bio/io/soapwsdl.rb - SOAP/WSDL interface class
+#
+# Copyright::   Copyright (C) 2004 
+#               KATAYAMA Toshiaki <k@bioruby.org>
+# License::     LGPL
+#
+# $Id: soapwsdl.rb,v 1.3 2005/12/18 16:51:18 nakao Exp $
+#
+# SOAP/WSDL 
+#
+#
+# == Examples
+# 
+# class API < Bio::SOAPWSDL
+#   def initialize
+#     @wsdl = 'http://example.com/example.wsdl'
+#     @log = File.new("soap_log", 'w')
+#     create_driver
+#   end
+# end
+#
+# == Use HTTP proxy
+#
+# You need to set following two environmental variables
+# (case might be insensitive) as required by SOAP4R.
+#
+# --- soap_use_proxy
+# Set the value of this variable to 'on'.
+#
+# --- http_proxy
+# Set the URL of your proxy server (http://myproxy.com:8080 etc.).
+#
+# === Example
+# 
+# % export soap_use_proxy=on
+# % export http_proxy=http://localhost:8080
+#
+#--
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#++
+#
+
+begin
+  require 'soap/wsdlDriver'
+rescue LoadError
+end
+
+module Bio
+
+class SOAPWSDL
+
+  # WSDL URL
+  attr_reader :wsdl
+
+  # log IO
+  attr_reader :log
+
+
+  def initialize(wsdl = nil)
+    @wsdl = wsdl
+    @log = nil
+    create_driver
+  end
+
+
+  def create_driver
+    if RUBY_VERSION > "1.8.2"
+      @driver = SOAP::WSDLDriverFactory.new(@wsdl).create_rpc_driver
+    else
+      @driver = SOAP::WSDLDriverFactory.new(@wsdl).create_driver
+    end
+    @driver.generate_explicit_type = true	# Ruby obj <-> SOAP obj
+  end
+  private :create_driver
+
+
+  # Set a WSDL URL.
+  def wsdl=(url)
+    @wsdl = url
+    create_driver
+  end
+
+
+  # Set log IO
+  def log=(io)
+    @log = io
+    @driver.wiredump_dev = @log
+  end
+
+
+  def method_missing(*arg)
+    @driver.send(*arg)
+  end
+  private :method_missing
+
+end # SOAP
+
+end # Bio
+

data/lib/bio/io/sql.rb

@@ -0,0 +1,428 @@
+#
+# bio/io/sql.rb - BioSQL access module
+#
+#   Copyright (C) 2002 KATAYAMA Toshiaki <k@bioruby.org>
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#  $Id: sql.rb,v 1.4 2005/09/26 13:04:28 k Exp $
+#
+
+begin
+  require 'dbi'
+rescue LoadError
+end
+require 'bio/sequence'
+require 'bio/feature'
+
+
+module Bio
+
+  class SQL
+
+    def initialize(db = 'dbi:Mysql:biosql', user = nil, pass = nil)
+      @dbh = DBI.connect(db, user, pass)
+    end
+
+    def close
+      @dbh.disconnect
+    end
+
+    def fetch(accession)	# or display_id for fall back
+      query = "select * from bioentry where accession = ?"
+      entry = @dbh.execute(query, accession).fetch
+      return Sequence.new(@dbh, entry) if entry
+
+      query = "select * from bioentry where display_id = ?"
+      entry = @dbh.execute(query, accession).fetch
+      return Sequence.new(@dbh, entry) if entry
+    end
+    alias get_by_id fetch
+
+
+    # for lazy fetching
+
+    class Sequence
+
+      def initialize(dbh, entry)
+        @dbh = dbh
+        @bioentry_id = entry['bioentry_id']
+        @database_id = entry['biodatabase_id']
+        @entry_id = entry['display_id']
+        @accession = entry['accession']
+        @version = entry['entry_version']
+        @division = entry['division']
+      end
+      attr_reader :accession, :division, :entry_id, :version
+
+
+      def to_fasta
+        if seq = seq
+          return seq.to_fasta(@accession)
+        end
+      end
+
+      def seq
+        query = "select * from biosequence where bioentry_id = ?"
+        row = @dbh.execute(query, @bioentry_id).fetch
+        return unless row
+
+        mol = row['molecule']
+        seq = row['biosequence_str']
+
+        case mol
+        when /.na/i			# 'dna' or 'rna'
+          Bio::Sequence::NA.new(seq)
+        else				# 'protein'
+          Bio::Sequence::AA.new(seq)
+        end
+      end
+
+      def subseq(from, to)
+        length = to - from + 1
+        query = "select molecule, substring(biosequence_str, ?, ?) as subseq" +
+                " from biosequence where bioentry_id = ?"
+        row = @dbh.execute(query, from, length, @bioentry_id).fetch
+        return unless row
+
+        mol = row['molecule']
+        seq = row['subseq']
+
+        case mol
+        when /.na/i			# 'dna' or 'rna'
+          Bio::Sequence::NA.new(seq)
+        else				# 'protein'
+          Bio::Sequence::AA.new(seq)
+        end
+      end
+
+
+      def features
+        array = []
+        query = "select * from seqfeature where bioentry_id = ?"
+        @dbh.execute(query, @bioentry_id).fetch_all.each do |row|
+          next unless row
+
+          f_id = row['seqfeature_id']
+          k_id = row['seqfeature_key_id']
+          s_id = row['seqfeature_source_id']
+          rank = row['seqfeature_rank'].to_i - 1
+
+          # key : type (gene, CDS, ...)
+          type = feature_key(k_id)
+
+          # source : database (EMBL/GenBank/SwissProt)
+          database = feature_source(s_id)
+
+          # location : position
+          locations = feature_locations(f_id)
+
+          # qualifier
+          qualifiers = feature_qualifiers(f_id)
+  
+          # rank
+          array[rank] = Bio::Feature.new(type, locations, qualifiers)
+        end
+        return Bio::Features.new(array)
+      end
+
+
+      def references
+        array = []
+        query = <<-END
+          select * from bioentry_reference, reference
+          where bioentry_id = ? and
+          bioentry_reference.reference_id = reference.reference_id
+        END
+        @dbh.execute(query, @bioentry_id).fetch_all.each do |row|
+          next unless row
+
+          hash = {
+            'start'	=> row['reference_start'],
+            'end'	=> row['reference_end'],
+            'journal'	=> row['reference_location'],
+            'title'	=> row['reference_title'],
+            'authors'	=> row['reference_authors'],
+            'medline'	=> row['reference_medline']
+          }
+          hash.default = ''
+
+          rank = row['reference_rank'].to_i - 1
+          array[rank] = hash
+        end
+        return array
+      end
+
+
+      def comment
+        query = "select * from comment where bioentry_id = ?"
+        row = @dbh.execute(query, @bioentry_id).fetch
+        row ? row['comment_text'] : ''
+      end
+
+      def comments
+        array = []
+        query = "select * from comment where bioentry_id = ?"
+        @dbh.execute(query, @bioentry_id).fetch_all.each do |row|
+          next unless row
+          rank = row['comment_rank'].to_i - 1
+          array[rank] = row['comment_text']
+        end
+        return array
+      end
+
+      def database
+        query = "select * from biodatabase where biodatabase_id = ?"
+        row = @dbh.execute(query, @database_id).fetch
+        row ? row['name'] : ''
+      end
+
+      def date
+        query = "select * from bioentry_date where bioentry_id = ?"
+        row = @dbh.execute(query, @bioentry_id).fetch
+        row ? row['date'] : ''
+      end
+
+      def dblink
+        query = "select * from bioentry_direct_links where source_bioentry_id = ?"
+        row = @dbh.execute(query, @bioentry_id).fetch
+        row ? [row['dbname'], row['accession']] : []
+      end
+
+      def definition
+        query = "select * from bioentry_description where bioentry_id = ?"
+        row = @dbh.execute(query, @bioentry_id).fetch
+        row ? row['description'] : ''
+      end
+
+      def keyword
+        query = "select * from bioentry_keywords where bioentry_id = ?"
+        row = @dbh.execute(query, @bioentry_id).fetch
+        row ? row['keywords'] : ''
+      end
+
+      def taxonomy
+        query = <<-END
+          select full_lineage, common_name, ncbi_taxa_id
+          from bioentry_taxa, taxa
+          where bioentry_id = ? and bioentry_taxa.taxa_id = taxa.taxa_id
+        END
+        row = @dbh.execute(query, @bioentry_id).fetch
+        @lineage = row ? row['full_lineage'] : ''
+        @common_name = row ? row['common_name'] : ''
+        @ncbi_taxa_id = row ? row['ncbi_taxa_id'] : ''
+        row ? [@lineage, @common_name, @ncbi_taxa_id] : []
+      end
+
+      def lineage
+        taxonomy unless @lineage
+        return @lineage
+      end
+
+      def common_name
+        taxonomy unless @common_name
+        return @common_name
+      end
+
+      def ncbi_taxa_id
+        taxonomy unless @ncbi_taxa_id
+        return @ncbi_taxa_id
+      end
+
+
+      private
+
+      def feature_key(k_id)
+        query = "select * from seqfeature_key where seqfeature_key_id = ?"
+        row = @dbh.execute(query, k_id).fetch
+        row ? row['key_name'] : ''
+      end
+
+      def feature_source(s_id)
+        query = "select * from seqfeature_source where seqfeature_source_id = ?"
+        row = @dbh.execute(query, s_id).fetch
+        row ? row['source_name'] : ''
+      end
+
+      def feature_locations(f_id)
+        locations = []
+        query = "select * from seqfeature_location where seqfeature_id = ?"
+        @dbh.execute(query, f_id).fetch_all.each do |row|
+          next unless row
+
+          location = Bio::Location.new
+          location.strand = row['seq_strand']
+          location.from = row['seq_start']
+          location.to = row['seq_end']
+
+          xref = feature_locations_remote(row['seqfeature_location_id'])
+          location.xref_id = xref.shift unless xref.empty?
+
+          # just omit fuzzy location for now...
+          #feature_locations_qv(row['seqfeature_location_id'])
+
+          rank = row['location_rank'].to_i - 1
+          locations[rank] = location
+        end
+        return Bio::Locations.new(locations)
+      end
+
+      def feature_locations_remote(l_id)
+        query = "select * from remote_seqfeature_name where seqfeature_location_id = ?"
+        row = @dbh.execute(query, l_id).fetch
+        row ? [row['accession'], row['version']] : []
+      end
+
+      def feature_locations_qv(l_id)
+        query = "select * from location_qualifier_value where seqfeature_location_id = ?"
+        row = @dbh.execute(query, l_id).fetch
+        row ? [row['qualifier_value'], row['slot_value']] : []
+      end
+
+      def feature_qualifiers(f_id)
+        qualifiers = []
+        query = "select * from seqfeature_qualifier_value where seqfeature_id = ?"
+        @dbh.execute(query, f_id).fetch_all.each do |row|
+          next unless row
+
+          key = feature_qualifiers_key(row['seqfeature_qualifier_id'])
+          value = row['qualifier_value']
+          qualifier = Bio::Feature::Qualifier.new(key, value)
+
+          rank = row['seqfeature_qualifier_rank'].to_i - 1
+          qualifiers[rank] = qualifier
+        end
+        return qualifiers.compact	# .compact is nasty hack for a while
+      end
+
+      def feature_qualifiers_key(q_id)
+        query = "select * from seqfeature_qualifier where seqfeature_qualifier_id = ?"
+        row = @dbh.execute(query, q_id).fetch
+        row ? row['qualifier_name'] : ''
+      end
+    end
+
+  end
+
+end
+
+
+if __FILE__ == $0
+  begin
+    require 'pp'
+    alias p pp
+  rescue LoadError
+  end
+
+  db = ARGV.empty? ? 'dbi:Mysql:database=biosql;host=localhost' : ARGV.shift
+  serv = Bio::SQL.new(db, 'root')
+
+  ent0 = serv.fetch('X76706')
+  ent0 = serv.fetch('A15H9FIB')
+  ent1 = serv.fetch('J01902')
+  ent2 = serv.fetch('X04311')
+
+  pp ent0.features
+  pp ent0.references
+
+  pp ent1.seq
+  pp ent1.seq.translate
+  pp ent1.seq.gc
+  pp ent1.subseq(1,20)
+
+  pp ent2.accession
+  pp ent2.comment
+  pp ent2.comments
+  pp ent2.common_name
+  pp ent2.database
+  pp ent2.date
+  pp ent2.dblink
+  pp ent2.definition
+  pp ent2.division
+  pp ent2.entry_id
+  pp ent2.features
+  pp ent2.keyword
+  pp ent2.lineage
+  pp ent2.ncbi_taxa_id
+  pp ent2.references
+  pp ent2.seq
+  pp ent2.subseq(1,10)
+  pp ent2.taxonomy
+  pp ent2.version
+
+end
+
+
+=begin
+
+= Bio::SQL
+
+--- Bio::SQL.new(db = 'dbi:Mysql:biosql', user = nil, pass = nil)
+
+--- Bio::SQL.close
+
+--- Bio::SQL#fetch(accession)
+
+      Returns Bio::SQL::Sequence object.
+
+== Bio::SQL::Sequence
+
+--- Bio::SQL::Sequence.new(dbh, entry)
+
+--- Bio::SQL::Sequence#accession -> String
+--- Bio::SQL::Sequence#comment -> String
+
+      Returns the first comment.  For complete comments, use comments method.
+
+--- Bio::SQL::Sequence#comments -> Array
+
+      Returns comments in an Array of Strings.
+
+--- Bio::SQL::Sequence#common_name -> String
+--- Bio::SQL::Sequence#database -> String
+--- Bio::SQL::Sequence#date -> String
+--- Bio::SQL::Sequence#dblink -> Array
+--- Bio::SQL::Sequence#definition -> String
+--- Bio::SQL::Sequence#division -> String
+--- Bio::SQL::Sequence#entry_id -> String
+
+--- Bio::SQL::Sequence#features
+
+      Returns Bio::Features object.
+
+--- Bio::SQL::Sequence#keyword -> String
+--- Bio::SQL::Sequence#lineage -> String
+--- Bio::SQL::Sequence#ncbi_taxa_id -> String
+
+--- Bio::SQL::Sequence#references -> Array
+
+      Returns reference informations in Array of Hash (not Bio::Reference).
+
+--- Bio::SQL::Sequence#seq
+
+      Returns Bio::Sequence::NA or AA object.
+
+--- Bio::SQL::Sequence#subseq(from, to)
+
+      Returns Bio::Sequence::NA or AA object (by lazy fetching).
+
+--- Bio::SQL::Sequence#taxonomy -> DBI::Row
+
+      Use lineage, common_name, ncbi_taxa_id methods to extract in detail.
+
+--- Bio::SQL::Sequence#version -> String
+
+=end
+