bio 1.2.1 → 1.3.0

data/lib/bio/db/fasta/defline.rb

@@ -0,0 +1,532 @@
+#
+# = bio/db/fasta/defline.rb - FASTA defline parser class
+#
+# Copyright::  Copyright (C) 2001, 2002
+#              GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>,
+#              Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
+#
+# $Id: defline.rb,v 1.1.2.1 2008/06/20 13:22:32 ngoto Exp $
+# 
+# == Description
+# 
+# Bio::FastaDefline is a parser class for definition line (defline)
+# of the FASTA format.
+#
+# == Examples
+#
+#       rub = Bio::FastaDefline.new('>gi|671595|emb|CAA85678.1| rubisco large subunit [Perovskia abrotanoides]')
+#       rub.entry_id       ==> 'gi|671595'
+#       rub.get('emb')     ==> 'CAA85678.1'
+#       rub.emb            ==> 'CAA85678.1'
+#       rub.gi             ==> '671595'
+#       rub.accession      ==> 'CAA85678'
+#       rub.accessions     ==> [ 'CAA85678' ]
+#       rub.acc_version    ==> 'CAA85678.1'
+#       rub.locus          ==> nil
+#       rub.list_ids       ==> [["gi", "671595"],
+#                               ["emb", "CAA85678.1", nil],
+#                               ["Perovskia abrotanoides"]]
+#
+#       ckr = Bio::FastaDefline.new(">gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)\001gi|2147182|pir||I51898 cholecystokinin A receptor - guinea pig\001gi|544724|gb|AAB29504.1| cholecystokinin A receptor; CCK-A receptor [Cavia]")
+#       ckr.entry_id      ==> "gi|2495000"
+#       ckr.sp            ==> "CCKR_CAVPO"
+#       ckr.pir           ==> "I51898"
+#       ckr.gb            ==> "AAB29504.1"
+#       ckr.gi            ==> "2495000"
+#       ckr.accession     ==> "AAB29504"
+#       ckr.accessions    ==> ["Q63931", "AAB29504"]
+#       ckr.acc_version   ==> "AAB29504.1"
+#       ckr.locus         ==> nil
+#       ckr.description   ==>
+#         "CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)"
+#       ckr.descriptions  ==>
+#         ["CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)",
+#          "cholecystokinin A receptor - guinea pig",
+#          "cholecystokinin A receptor; CCK-A receptor [Cavia]"]
+#       ckr.words         ==> 
+#         ["cavia", "cck-a", "cck-ar", "cholecystokinin", "guinea", "pig",
+#          "receptor", "type"]
+#       ckr.id_strings    ==>
+#         ["2495000", "Q63931", "CCKR_CAVPO", "2147182", "I51898",
+#          "544724", "AAB29504.1", "Cavia"]
+#       ckr.list_ids      ==>
+#         [["gi", "2495000"], ["sp", "Q63931", "CCKR_CAVPO"],
+#          ["gi", "2147182"], ["pir", nil, "I51898"], ["gi", "544724"],
+#          ["gb", "AAB29504.1", nil], ["Cavia"]]
+#
+# == References
+#
+# * FASTA format (WikiPedia)
+#   http://en.wikipedia.org/wiki/FASTA_format
+#   
+# * Fasta format description (NCBI)
+#   http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml
+#
+
+module Bio
+
+  #--
+  # split from fasta.rb revision 1.28
+  #++
+
+  # Parsing FASTA Defline, and extract IDs and other informations.
+  # IDs are NSIDs (NCBI standard FASTA sequence identifiers)
+  # or ":"-separated IDs.
+  # 
+  # specs are described in:
+  # ftp://ftp.ncbi.nih.gov/blast/documents/README.formatdb
+  # http://blast.wustl.edu/doc/FAQ-Indexing.html#Identifiers
+  #
+  # === Examples
+  #
+  #   rub = Bio::FastaDefline.new('>gi|671595|emb|CAA85678.1| rubisco large subunit [Perovskia abrotanoides]')
+  #   rub.entry_id       ==> 'gi|671595'
+  #   rub.get('emb')     ==> 'CAA85678.1'
+  #   rub.emb            ==> 'CAA85678.1'
+  #   rub.gi             ==> '671595'
+  #   rub.accession      ==> 'CAA85678'
+  #   rub.accessions     ==> [ 'CAA85678' ]
+  #   rub.acc_version    ==> 'CAA85678.1'
+  #   rub.locus          ==> nil
+  #   rub.list_ids       ==> [["gi", "671595"],
+  #                           ["emb", "CAA85678.1", nil],
+  #                           ["Perovskia abrotanoides"]]
+  #
+  #   ckr = Bio::FastaDefline.new(">gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)\001gi|2147182|pir||I51898 cholecystokinin A receptor - guinea pig\001gi|544724|gb|AAB29504.1| cholecystokinin A receptor; CCK-A receptor [Cavia]")
+  #   ckr.entry_id      ==> "gi|2495000"
+  #   ckr.sp            ==> "CCKR_CAVPO"
+  #   ckr.pir           ==> "I51898"
+  #   ckr.gb            ==> "AAB29504.1"
+  #   ckr.gi            ==> "2495000"
+  #   ckr.accession     ==> "AAB29504"
+  #   ckr.accessions    ==> ["Q63931", "AAB29504"]
+  #   ckr.acc_version   ==> "AAB29504.1"
+  #   ckr.locus         ==> nil
+  #   ckr.description   ==>
+  #     "CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)"
+  #   ckr.descriptions  ==>
+  #     ["CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)",
+  #      "cholecystokinin A receptor - guinea pig",
+  #      "cholecystokinin A receptor; CCK-A receptor [Cavia]"]
+  #   ckr.words         ==> 
+  #     ["cavia", "cck-a", "cck-ar", "cholecystokinin", "guinea", "pig",
+  #      "receptor", "type"]
+  #   ckr.id_strings    ==>
+  #     ["2495000", "Q63931", "CCKR_CAVPO", "2147182", "I51898",
+  #      "544724", "AAB29504.1", "Cavia"]
+  #   ckr.list_ids      ==>
+  #     [["gi", "2495000"], ["sp", "Q63931", "CCKR_CAVPO"],
+  #      ["gi", "2147182"], ["pir", nil, "I51898"], ["gi", "544724"],
+  #      ["gb", "AAB29504.1", nil], ["Cavia"]]
+  #
+  # === Refereneces
+  #
+  # * Fasta format description (NCBI)
+  #   http://www.ncbi.nlm.nih.gov/BLAST/fasta.shtml
+  #
+  # * Frequently Asked Questions:  Indexing of Sequence Identifiers (by Warren R. Gish.)
+  #   http://blast.wustl.edu/doc/FAQ-Indexing.html#Identifiers
+  #
+  # * README.formatdb
+  #   ftp://ftp.ncbi.nih.gov/blast/documents/README.formatdb
+  # 
+  class FastaDefline
+
+    NSIDs = {
+      # NCBI and WU-BLAST
+      'gi'  => [ 'gi' ],                      # NCBI GI
+      'gb'  => [ 'acc_version', 'locus' ],      # GenBank
+      'emb' => [ 'acc_version', 'locus' ],      # EMBL
+      'dbj' => [ 'acc_version', 'locus' ],      # DDBJ
+      'sp'  => [ 'accession', 'entry_id' ],   # SWISS-PROT
+      'pdb' => [ 'entry_id', 'chain' ],       # PDB
+      'bbs' => [ 'number' ],                  # GenInfo Backbone Id
+      'gnl' => [ 'database' , 'entry_id' ],   # General database identifier
+      'ref' => [ 'acc_version' , 'locus' ],     # NCBI Reference Sequence
+      'lcl' => [ 'entry_id' ],                # Local Sequence identifier
+
+      # WU-BLAST and NCBI
+      'pir' => [ 'accession', 'entry_id' ],   # PIR
+      'prf' => [ 'accession', 'entry_id' ],   # Protein Research Foundation
+      'pat' => [ 'country', 'number', 'serial' ], # Patents
+
+      # WU-BLAST only
+      'bbm' => [ 'number' ],      # NCBI GenInfo Backbone database identifier
+      'gim' => [ 'number' ],      # NCBI GenInfo Import identifier
+      'gp'  => [ 'acc_version', 'locus' ],      # GenPept
+      'oth' => [ 'accession', 'name', 'release' ],  # Other (user-definable) identifier
+      'tpd' => [ 'accession', 'name' ],       # Third party annotation, DDBJ
+      'tpe' => [ 'accession', 'name' ],       # Third party annotation, EMBL
+      'tpg' => [ 'accession', 'name' ],       # Third party annotation, GenBank
+
+      # Original
+      'ri'  => [ 'entry_id', 'rearray_id', 'len' ], # RIKEN FANTOM DB
+    }
+
+    # Shows array that contains IDs (or ID-like strings).
+    # Returns an array of arrays of strings.
+    attr_reader :list_ids
+
+    # Shows a possibly unique identifier.
+    # Returns a string.
+    attr_reader :entry_id
+
+    # Parses given string.
+    def initialize(str)
+      @deflines = []
+      @info = {}
+      @list_ids = []
+
+      @entry_id = nil
+
+      lines = str.split("\x01")
+      lines.each do |line|
+        add_defline(line)
+      end
+    end #def initialize
+
+    # Parses given string and adds parsed data.
+    def add_defline(str)
+      case str
+      when /^\>?\s*((?:[^\|\s]*\|)+[^\s]+)\s*(.*)$/
+        # NSIDs
+        # examples:
+        # >gi|9910844|sp|Q9UWG2|RL3_METVA 50S ribosomal protein L3P
+        #
+        # note: regexp (:?) means grouping without backreferences
+        i = $1
+        d = $2
+        tks = i.split('|')
+        tks << '' if i[-1,1] == '|'
+        a = parse_NSIDs(tks)
+        i = a[0].join('|')
+        a.unshift('|')
+        d = tks.join('|') + ' ' + d unless tks.empty?
+        a << d
+        this_line = a
+        match_EC(d)
+        parse_square_brackets(d).each do |x|
+          if !match_EC(x, false) and x =~ /\A[A-Z]/ then
+            di = [  x ]
+            @list_ids << di
+            @info['organism'] = x unless @info['organism']
+          end
+        end
+
+      when /^\>?\s*([a-zA-Z0-9]+\:[^\s]+)\s*(.*)$/
+        # examples:
+        # >sce:YBR160W  CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
+        # >emb:CACDC28 [X80034] C.albicans CDC28 gene 
+        i = $1
+        d = $2
+        a = parse_ColonSepID(i)
+        i = a.join(':')
+        this_line = [ ':', a , d ]
+        match_EC(d)
+        parse_square_brackets(d).each do |x|
+          if !match_EC(x, false) and x =~ /:/ then
+            parse_ColonSepID(x)
+          elsif x =~ /\A\s*([A-Z][A-Z0-9_\.]+)\s*\z/ then
+            @list_ids << [ $1 ]
+          end
+        end
+
+      when /^\>?\s*(\S+)(?:\s+(.+))?$/
+        # examples:
+        # >ABC12345 this is test
+        i = $1
+        d = $2.to_s
+        @list_ids << [ i.chomp('.') ]
+        this_line = [  '', [ i ], d ]
+        match_EC(d)
+      else
+        i = str
+        d = ''
+        match_EC(i)
+        this_line = [ '', [ i ], d ]
+      end
+
+      @deflines << this_line
+      @entry_id = i unless @entry_id
+    end
+
+    def match_EC(str, write_flag = true)
+      di = nil
+      str.scan(/EC\:((:?[\-\d]+\.){3}(:?[\-\d]+))/i) do |x|
+        di = [ 'EC', $1 ]
+        if write_flag then
+          @info['ec'] = di[1] if (!@info['ec'] or @info['ec'].to_s =~ /\-/)
+          @list_ids << di
+        end
+      end
+      di
+    end
+    private :match_EC
+
+    def parse_square_brackets(str)
+      r = []
+      str.scan(/\[([^\]]*)\]/) do |x|
+        r << x[0]
+      end
+      r
+    end
+    private :parse_square_brackets
+
+    def parse_ColonSepID(str)
+      di = str.split(':', 2)
+      di << nil if di.size <= 1 
+      @list_ids << di
+      di
+    end
+    private :parse_ColonSepID
+
+    def parse_NSIDs(ary)
+      # this method destroys ary
+      data = []
+      while token = ary.shift
+        if labels = self.class::NSIDs[token] then
+          di = [ token ]
+          idtype = token
+          labels.each do |x|
+            token = ary.shift
+            break unless token
+            if self.class::NSIDs[token] then
+              ary.unshift(token)
+              break #each
+            end
+            if token.length > 0 then
+              di << token
+            else
+              di << nil
+            end
+          end
+          data << di
+        else
+          if token.length > 0 then
+            # UCID (uncontrolled identifiers)
+            di = [ token ]
+            data << di
+            @info['ucid'] = token unless @info['ucid']
+          end
+          break #while
+        end
+      end #while
+      @list_ids.concat data
+      data
+    end #def parse_NSIDs
+    private :parse_NSIDs
+
+
+    # Shows original string.
+    # Note that the result of this method may be different from
+    # original string which is given in FastaDefline.new method.
+    def to_s
+      @deflines.collect { |a|
+        s = a[0]
+        (a[1..-2].collect { |x| x.join(s) }.join(s) + ' ' + a[-1]).strip
+      }.join("\x01")
+    end
+
+    # Shows description.
+    def description
+      @deflines[0].to_a[-1]
+    end
+
+    # Returns descriptions.
+    def descriptions
+      @deflines.collect do |a|
+        a[-1]
+      end
+    end
+
+    # Shows ID-like strings.
+    # Returns an array of strings.
+    def id_strings
+      r = []
+      @list_ids.each do |a|
+        if a.size >= 2 then
+          r.concat a[1..-1].find_all { |x| x }
+        else
+          if a[0].to_s.size > 0 and a[0] =~ /\A[A-Za-z0-9\.\-\_]+\z/
+            r << a[0]
+          end
+        end
+      end
+      r.concat( words(true, []).find_all do |x|
+                 x =~ /\A[A-Z][A-Za-z0-9\_]*[0-9]+[A-Za-z0-9\_]+\z/ or
+                   x =~ /\A[A-Z][A-Z0-9]*\_[A-Z0-9\_]+\z/
+               end)
+      r
+    end
+
+    KillWords = [
+      'an', 'the', 'this', 'that',
+      'is', 'are', 'were', 'was', 'be', 'can', 'may', 'might',
+      'as', 'at', 'by', 'for', 'in', 'of', 'on', 'to', 'with',
+      'from', 'and', 'or', 'not',
+      'dna', 'rna', 'mrna', 'cdna', 'orf',
+      'aa', 'nt', 'pct', 'id', 'ec', 'sp', 'subsp',
+      'similar', 'involved', 'identical', 'identity',
+      'cds', 'clone', 'library', 'contig', 'contigs',
+      'homolog', 'homologue', 'homologs', 'homologous',
+      'protein', 'proteins', 'gene', 'genes',
+      'product', 'products', 'sequence', 'sequences', 
+      'strain', 'strains', 'region', 'regions',
+    ]
+    KillWordsHash = {}
+    KillWords.each { |x| KillWordsHash[x] = true }
+
+    KillRegexpArray = [
+      /\A\d{1,3}\%?\z/,
+      /\A[A-Z][A-Za-z0-9\_]*[0-9]+[A-Za-z0-9\_]+\z/,
+      /\A[A-Z][A-Z0-9]*\_[A-Z0-9\_]+\z/
+    ]
+
+    # Shows words used in the defline. Returns an Array.
+    def words(case_sensitive = nil, kill_regexp = self.class::KillRegexpArray,
+              kwhash = self.class::KillWordsHash)
+      a = descriptions.join(' ').split(/[\.\,\;\:\(\)\[\]\{\}\<\>\"\'\`\~\/\|\?\!\&\@\#\s\x00-\x1f\x7f]+/)
+      a.collect! do |x|
+        x.sub!(/\A[\$\*\-\+]+/, '')
+        x.sub!(/[\$\*\-\=]+\z/, '')
+        if x.size <= 1 then
+          nil
+        elsif kwhash[x.downcase] then
+          nil
+        else
+          if kill_regexp.find { |expr| expr =~ x } then
+            nil
+          else
+            x
+          end
+        end
+      end
+      a.compact!
+      a.collect! { |x| x.downcase } unless case_sensitive
+      a.sort!
+      a.uniq!
+      a
+    end
+
+    # Returns identifires by a database name.
+    def get(dbname)
+      db = dbname.to_s
+      r = nil
+      unless r = @info[db] then
+        di = @list_ids.find { |x| x[0] == db.to_s }
+        if di and di.size <= 2 then
+          r = di[-1]
+        elsif di then
+          labels = self.class::NSIDs[db]
+          [ 'acc_version', 'entry_id',
+            'locus', 'accession', 'number'].each do |x|
+            if i = labels.index(x) then
+              r = di[i+1]
+              break if r
+            end
+          end
+          r = di[1..-1].find { |x| x } unless r
+        end
+        @info[db] = r if r
+      end
+      r
+    end
+
+    # Returns an identifier by given type.
+    def get_by_type(type_str)
+      @list_ids.each do |x|
+        if labels = self.class::NSIDs[x[0]] then
+          if i = labels.index(type_str) then
+            return x[i+1]
+          end
+        end
+      end
+      nil
+    end
+
+    # Returns identifiers by given type.
+    def get_all_by_type(*type_strarg)
+      d = []
+      @list_ids.each do |x|
+        if labels = self.class::NSIDs[x[0]] then
+          type_strarg.each do |y|
+            if i = labels.index(y) then
+              d << x[i+1] if x[i+1]
+            end
+          end
+        end
+      end
+      d
+    end
+
+    # Shows locus.
+    # If the entry has more than two of such IDs,
+    # only the first ID are shown.
+    # Returns a string or nil.
+    def locus
+      unless defined?(@locus)
+        @locus = get_by_type('locus')
+      end
+      @locus
+    end
+
+    # Shows GI.
+    # If the entry has more than two of such IDs,
+    # only the first ID are shown.
+    # Returns a string or nil.
+    def gi
+      unless defined?(@gi) then
+        @gi = get_by_type('gi')
+      end
+      @gi
+    end
+
+    # Shows accession with version number.
+    # If the entry has more than two of such IDs,
+    # only the first ID are shown.
+    # Returns a string or nil.
+    def acc_version
+      unless defined?(@acc_version) then
+        @acc_version = get_by_type('acc_version')
+      end
+      @acc_version
+    end
+
+    # Shows accession numbers.
+    # Returns an array of strings.
+    def accessions
+      unless defined?(@accessions) then
+        @accessions = get_all_by_type('accession', 'acc_version')
+        @accessions.collect! { |x| x.sub(/\..*\z/, '') }
+      end
+      @accessions
+    end
+
+    # Shows an accession number.
+    def accession
+      unless defined?(@accession) then
+        if acc_version then
+          @accession = acc_version.split('.')[0]
+        else
+          @accession = accessions[0]
+        end
+      end
+      @accession
+    end
+    
+    def method_missing(name, *args)
+      # raise ArgumentError,
+      # "wrong # of arguments(#{args.size} for 1)" if args.size >= 2
+      r = get(name, *args)
+      if !r and !(self.class::NSIDs[name.to_s]) then
+        raise "NameError: undefined method `#{name.inspect}'"
+      end
+      r
+    end
+    
+
+  end #class FastaDefline
+
+end #module Bio
+