ngoto-bio 1.2.9.9001

data/lib/bio/db/embl/common.rb

@@ -0,0 +1,352 @@
+#
+# = bio/db/embl.rb - Common methods for EMBL style database classes
+#
+# Copyright::   Copyright (C) 2001-2006
+#               Mitsuteru C. Nakao <n@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: common.rb,v 1.12.2.5 2008/05/07 12:22:10 ngoto Exp $
+#
+# == Description
+#
+# EMBL style databases class
+#
+# This module defines a common framework among EMBL, UniProtKB, SWISS-PROT, 
+# TrEMBL. For more details, see the documentations in each embl/*.rb 
+# libraries.
+#
+# EMBL style format:
+#     ID - identification             (begins each entry; 1 per entry)
+#     AC - accession number           (>=1 per entry)
+#     SV - sequence version           (1 per entry)
+#     DT - date                       (2 per entry)
+#     DE - description                (>=1 per entry)
+#     KW - keyword                    (>=1 per entry)
+#     OS - organism species           (>=1 per entry)
+#     OC - organism classification    (>=1 per entry)
+#     OG - organelle                  (0 or 1 per entry)
+#     RN - reference number           (>=1 per entry)
+#     RC - reference comment          (>=0 per entry)
+#     RP - reference positions        (>=1 per entry)
+#     RX - reference cross-reference  (>=0 per entry)
+#     RA - reference author(s)        (>=1 per entry)
+#     RG - reference group            (>=0 per entry)
+#     RT - reference title            (>=1 per entry)
+#     RL - reference location         (>=1 per entry)
+#     DR - database cross-reference   (>=0 per entry)
+#     FH - feature table header       (0 or 2 per entry)
+#     FT - feature table data         (>=0 per entry)
+#     CC - comments or notes          (>=0 per entry)
+#     XX - spacer line                (many per entry)
+#     SQ - sequence header            (1 per entry)
+#     bb - (blanks) sequence data     (>=1 per entry)
+#     // - termination line           (ends each entry; 1 per entry)
+#
+# == Examples
+# 
+#  # Make a new parser class for EMBL style database entry.
+#  require 'bio/db/embl/common'
+#  module Bio
+#    class NEWDB < EMBLDB
+#      include Bio::EMBLDB::Common
+#    end
+#  end
+#
+# == References
+#
+# * The EMBL Nucleotide Sequence Database
+#   http://www.ebi.ac.uk/embl/
+#
+# * The EMBL Nucleotide Sequence Database: Users Manual
+#   http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
+# 
+# * Swiss-Prot Protein knowledgebase. TrEMBL Computer-annotated supplement 
+#   to Swiss-Prot 
+#   http://au.expasy.org/sprot/
+# 
+# * UniProt 
+#   http://uniprot.org/
+# 
+# * The UniProtKB/SwissProt/TrEMBL User Manual 
+#   http://www.expasy.org/sprot/userman.html
+#
+
+require 'bio/db'
+require 'bio/reference'
+require 'bio/compat/references'
+
+module Bio
+class EMBLDB
+module Common
+
+  DELIMITER = "\n//\n"
+  RS = DELIMITER
+  TAGSIZE = 5
+
+  def initialize(entry)
+    super(entry, TAGSIZE)
+  end
+
+  # returns a Array of accession numbers in the AC lines.
+  #
+  # AC Line
+  #   "AC   A12345; B23456;"
+  #   AC [AC1;]+
+  #
+  # Accession numbers format:
+  #   1       2     3          4          5          6
+  #   [O,P,Q] [0-9] [A-Z, 0-9] [A-Z, 0-9] [A-Z, 0-9] [0-9]
+  def ac
+    unless @data['AC']
+      tmp = Array.new
+      field_fetch('AC').split(/ /).each do |e|
+        tmp.push(e.sub(/;/,''))
+      end
+      @data['AC'] = tmp
+    end
+    @data['AC']
+  end
+  alias accessions ac
+
+
+  # returns the first accession number in the AC lines
+  def accession
+    ac[0]
+  end
+
+
+  # returns a String int the DE line.
+  #
+  # DE Line
+  def de
+    unless @data['DE']
+      @data['DE'] = fetch('DE')
+    end
+    @data['DE']
+  end
+  alias description de
+  alias definition de   # API
+  
+
+
+  # returns contents in the OS line.
+  # * Bio::EMBLDB#os  -> Array of <OS Hash>
+  # where <OS Hash> is:
+  #  [{'name'=>'Human', 'os'=>'Homo sapiens'}, 
+  #   {'name'=>'Rat', 'os'=>'Rattus norveticus'}]
+  # * Bio::SPTR#os[0]['name'] => "Human"
+  # * Bio::SPTR#os[0] => {'name'=>"Human", 'os'=>'Homo sapiens'}
+  # * Bio::STPR#os(0) => "Homo sapiens (Human)"
+  #
+  # OS Line; organism species (>=1)
+  #   "OS   Trifolium repens (white clover)"
+  #
+  #   OS   Genus species (name).
+  #   OS   Genus species (name0) (name1).
+  #   OS   Genus species (name0) (name1).
+  #   OS   Genus species (name0), G s0 (name0), and G s (name1).
+  def os(num = nil)
+    unless @data['OS']
+      os = Array.new
+      fetch('OS').split(/, and|, /).each do |tmp|
+        if tmp =~ /([A-Z][a-z]* *[\w\d \:\'\+\-]+[\w\d])/
+          org = $1
+          tmp =~ /(\(.+\))/ 
+          os.push({'name' => $1, 'os' => org})
+        else
+          raise "Error: OS Line. #{$!}\n#{fetch('OS')}\n"
+        end
+      end
+      @data['OS'] = os
+    end
+    if num
+      # EX. "Trifolium repens (white clover)"
+      "#{@data['OS'][num]['os']} {#data['OS'][num]['name']"
+    end
+    @data['OS']
+  end
+
+
+  # returns contents in the OG line.
+  # * Bio::EMBLDB::Common#og  -> [ <ogranella String>* ]
+  #
+  # OG Line; organella (0 or 1/entry)
+  #  OG   Plastid; Chloroplast.
+  #  OG   Mitochondrion.
+  #  OG   Plasmid sym pNGR234a.
+  #  OG   Plastid; Cyanelle.
+  #  OG   Plasmid pSymA (megaplasmid 1).
+  #  OG   Plasmid pNRC100, Plasmid pNRC200, and Plasmid pHH1.
+  def og
+    unless @data['OG']
+      og = Array.new
+      if get('OG').size > 0
+        ogstr = fetch('OG')
+        ogstr.sub!(/\.$/,'')
+        ogstr.sub!(/ and/,'')
+        ogstr.sub!(/;/, ',')
+        ogstr.split(',').each do |tmp|
+          og.push(tmp.strip)
+        end
+      end
+      @data['OG'] = og
+    end
+    @data['OG']
+  end
+  
+
+  # returns contents in the OC line.
+  # * Bio::EMBLDB::Common#oc  -> [ <organism class String>* ]
+  # OC Line; organism classification (>=1)
+  #  OC   Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae;
+  #  OC   Theileria.
+  def oc
+    unless @data['OC']
+      begin
+        @data['OC'] = fetch('OC').sub(/.$/,'').split(/;/).map {|e|
+          e.strip 
+        }
+      rescue NameError
+        nil
+      end
+    end
+    @data['OC']
+  end
+
+  # returns keywords in the KW line.
+  # * Bio::EMBLDB::Common#kw  -> [ <keyword>* ]
+  # KW Line; keyword (>=1)
+  #  KW   [Keyword;]+
+  def kw
+    unless @data['KW']
+      if get('KW').size > 0
+        tmp = fetch('KW').sub(/.$/,'')
+        @data['KW'] = tmp.split(/;/).map {|e| e.strip }
+      else
+        @data['KW'] = []
+      end
+    end
+    @data['KW']
+  end
+  alias keywords kw
+
+
+  # returns contents in the R lines.
+  # * Bio::EMBLDB::Common#ref -> [ <refernece information Hash>* ]
+  # where <reference information Hash> is:
+  #  {'RN' => '', 'RC' => '', 'RP' => '', 'RX' => '', 
+  #   'RA' => '', 'RT' => '', 'RL' => '', 'RG' => ''}
+  # 
+  # R Lines
+  # * RN RC RP RX RA RT RL RG
+  def ref
+    unless @data['R']
+      ary = Array.new
+      get('R').split(/\nRN   /).each do |str|
+        raw = {'RN' => '', 'RC' => '', 'RP' => '', 'RX' => '', 
+               'RA' => '', 'RT' => '', 'RL' => '', 'RG' => ''}
+        str = 'RN   ' + str unless /^RN   / =~ str
+        str.split("\n").each do |line|
+          if /^(R[NPXARLCTG])   (.+)/ =~ line
+            raw[$1] += $2 + ' '
+          else
+            raise "Invalid format in R lines, \n[#{line}]\n"
+          end
+        end
+        raw.each_value {|v| 
+          v.strip! 
+          v.sub!(/^"/,'')
+          v.sub!(/;$/,'')
+          v.sub!(/"$/,'')
+        }
+        ary.push(raw)
+      end
+      @data['R'] = ary
+    end
+    @data['R']
+  end
+
+  # returns Bio::Reference object from Bio::EMBLDB::Common#ref.
+  # * Bio::EMBLDB::Common#ref -> Bio::References
+  def references
+    unless @data['references']
+      ary = self.ref.map {|ent|
+        hash = Hash.new
+        ent.each {|key, value|
+          case key
+          when 'RN'
+            if /\[(\d+)\]/ =~ value.to_s
+              hash['embl_gb_record_number'] = $1.to_i
+            end
+          when 'RC'
+            unless value.to_s.strip.empty?
+              hash['comments'] ||= []
+              hash['comments'].push value
+            end
+          when 'RP'
+            hash['sequence_position'] = value
+          when 'RA'
+            a = value.split(/\, /)
+            a.each do |x|
+              x.sub!(/( [^ ]+)\z/, ",\\1")
+            end
+            hash['authors'] = a
+          when 'RT'
+            hash['title'] = value
+          when 'RL'
+            if /(.*) (\d+) *(\(([^\)]+)\))?(\, |\:)([a-zA-Z\d]+\-[a-zA-Z\d]+) *\((\d+)\)\.?\z/ =~ value.to_s
+              hash['journal'] = $1.rstrip
+              hash['volume']  = $2
+              hash['issue']   = $4
+              hash['pages']   = $6
+              hash['year']    = $7
+            else
+              hash['journal'] = value
+            end
+          when 'RX'  # PUBMED, DOI, (AGRICOLA)
+            value.split(/\. /).each {|item|
+              tag, xref = item.split(/\; /).map {|i| i.strip.sub(/\.\z/, '') }
+              hash[ tag.downcase ]  = xref
+            }
+          end
+        }
+        Reference.new(hash)
+      }
+      @data['references'] = ary.extend(Bio::References::BackwardCompatibility)
+    end
+    @data['references']
+  end
+
+
+  # returns contents in the DR line.
+  # * Bio::EMBLDB::Common#dr  -> [ <Database cross-reference Hash>* ]
+  # where <Database cross-reference Hash> is:
+  # * Bio::EMBLDB::Common#dr {|k,v| } 
+  # 
+  # DR Line; defabases cross-reference (>=0)
+  # a cross_ref pre one line
+  #  "DR  database_identifier; primary_identifier; secondary_identifier."
+  def dr
+    unless @data['DR']
+      tmp = Hash.new
+      self.get('DR').split(/\n/).each do |db|
+        a = db.sub(/^DR   /,'').sub(/.$/,'').strip.split(/;[ ]/)
+        dbname = a.shift
+        tmp[dbname] = Array.new unless tmp[dbname]
+        tmp[dbname].push(a)
+      end
+      @data['DR'] = tmp
+    end
+    if block_given?
+      @data['DR'].each do |k,v|
+        yield(k, v)
+      end
+    else
+      @data['DR']
+    end
+  end
+
+end # module Common
+end # class EMBLDB
+end # module Bio
+