jandot-bio 1.2.1

data/lib/bio/appl/blast/xmlparser.rb

@@ -0,0 +1,228 @@
+#
+# = bio/appl/blast/xmlparser.rb - BLAST XML output (-m 7) parser by XMLParser
+# 
+# Copyright::  Copyright (C) 2001 
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# Copyright::  Copyright (C) 2003 
+#              Toshiaki Katayama <k@bioruby.org>
+# License::    The Ruby License
+#
+# $Id: xmlparser.rb,v 1.18 2008/05/12 13:11:45 ngoto Exp $
+#
+# == Description
+# 
+# A parser for blast XML report (format 7) based on the XMLParser.
+# This file is automatically loaded by bio/appl/blast/report.rb if
+# the XMLParser installed.
+#
+# BioRuby provides two implements of the paser for the blast XML format report
+# (format 7) based on the XMLParser and the REXML.
+#
+
+begin
+  require 'xmlparser'
+rescue LoadError
+end
+
+module Bio
+class Blast
+  class Report
+
+    private
+
+    def xmlparser_parse(xml)
+      parser = XMLParser.new
+      def parser.default; end
+       
+      begin
+        tag_stack = Array.new
+        hash = Hash.new
+
+        parser.parse(xml) do |type, name, data|
+          case type
+          when XMLParser::START_ELEM
+            tag_stack.push(name)
+            hash.update(data)
+            case name
+            when 'Iteration'
+              iteration = Iteration.new
+              @iterations.push(iteration)
+            when 'Hit'
+              hit = Hit.new
+              hit.query_id = @query_id
+              hit.query_def = @query_def
+              hit.query_len = @query_len
+              @iterations.last.hits.push(hit)
+            when 'Hsp'
+              hsp = Hsp.new
+              @iterations.last.hits.last.hsps.push(hsp)
+            end
+          when XMLParser::END_ELEM
+            case name
+            when /^BlastOutput/
+              xmlparser_parse_program(name,hash)
+              hash = Hash.new
+            when /^Parameters$/
+              xmlparser_parse_parameters(hash)
+              hash = Hash.new
+            when /^Iteration/
+              xmlparser_parse_iteration(name, hash)
+              hash = Hash.new
+            when /^Hit/
+              xmlparser_parse_hit(name, hash)
+              hash = Hash.new
+            when /^Hsp$/
+              xmlparser_parse_hsp(hash)
+              hash = Hash.new
+            when /^Statistics$/
+              xmlparser_parse_statistics(hash)
+              hash = Hash.new
+            end
+            tag_stack.pop
+          when XMLParser::CDATA
+            if hash[tag_stack.last].nil?
+              hash[tag_stack.last] = data unless data.strip.empty?
+            else
+              hash[tag_stack.last].concat(data) if data
+            end
+          when XMLParser::PI
+          end
+        end
+      rescue XMLParserError
+        line = parser.line
+        column = parser.column
+        print "Parse error at #{line}(#{column}) : #{$!}\n"
+      end
+    end
+
+
+    def xmlparser_parse_program(tag, hash)
+      case tag
+      when 'BlastOutput_program'
+        @program = hash[tag]
+      when 'BlastOutput_version'
+        @version = hash[tag]
+      when 'BlastOutput_reference'
+        @reference = hash[tag]
+      when 'BlastOutput_db'
+        @db = hash[tag].strip
+      when 'BlastOutput_query-ID'
+        @query_id = hash[tag]
+      when 'BlastOutput_query-def'
+        @query_def = hash[tag]
+      when 'BlastOutput_query-len'
+        @query_len = hash[tag].to_i
+      end
+    end
+
+    # set parameter of the key as val
+    def xml_set_parameter(key, val)
+      #labels = { 
+      #  'matrix'       => 'Parameters_matrix',
+      #  'expect'       => 'Parameters_expect',
+      #  'include'      => 'Parameters_include',
+      #  'sc-match'     => 'Parameters_sc-match',
+      #  'sc-mismatch'  => 'Parameters_sc-mismatch',
+      #  'gap-open'     => 'Parameters_gap-open',
+      #  'gap-extend'   => 'Parameters_gap-extend',
+      #  'filter'       => 'Parameters_filter',
+      #  'pattern'      => 'Parameters_pattern',
+      #  'entrez-query' => 'Parameters_entrez-query',
+      #}
+      k = key.sub(/\AParameters\_/, '')
+      @parameters[k] =
+        case k
+        when 'expect', 'include'
+          val.to_f
+        when /\Agap\-/, /\Asc\-/
+          val.to_i
+        else
+          val
+        end
+    end
+
+    def xmlparser_parse_parameters(hash)
+      hash.each do |k, v|
+        xml_set_parameter(k, v)
+      end
+    end
+
+    def xmlparser_parse_iteration(tag, hash)
+      case tag
+      when 'Iteration_iter-num'
+        @iterations.last.num = hash[tag].to_i
+      when 'Iteration_message'
+        @iterations.last.message = hash[tag].to_s
+      end
+    end
+
+    def xmlparser_parse_hit(tag, hash)
+      hit = @iterations.last.hits.last
+      case tag
+      when 'Hit_num'
+        hit.num = hash[tag].to_i
+      when 'Hit_id'
+        hit.hit_id = hash[tag].clone
+      when 'Hit_def'
+        hit.definition = hash[tag].clone
+      when 'Hit_accession'
+        hit.accession = hash[tag].clone
+      when 'Hit_len'
+        hit.len = hash[tag].clone.to_i
+      end
+    end
+
+    def xmlparser_parse_hsp(hash)
+      hsp = @iterations.last.hits.last.hsps.last
+      hsp.num          = hash['Hsp_num'].to_i
+      hsp.bit_score    = hash['Hsp_bit-score'].to_f
+      hsp.score        = hash['Hsp_score'].to_i
+      hsp.evalue       = hash['Hsp_evalue'].to_f
+      hsp.query_from   = hash['Hsp_query-from'].to_i
+      hsp.query_to     = hash['Hsp_query-to'].to_i
+      hsp.hit_from     = hash['Hsp_hit-from'].to_i
+      hsp.hit_to       = hash['Hsp_hit-to'].to_i
+      hsp.pattern_from = hash['Hsp_pattern-from'].to_i
+      hsp.pattern_to   = hash['Hsp_pattern-to'].to_i
+      hsp.query_frame  = hash['Hsp_query-frame'].to_i
+      hsp.hit_frame    = hash['Hsp_hit-frame'].to_i
+      hsp.identity     = hash['Hsp_identity'].to_i
+      hsp.positive     = hash['Hsp_positive'].to_i
+      hsp.gaps         = hash['Hsp_gaps'].to_i
+      hsp.align_len    = hash['Hsp_align-len'].to_i
+      hsp.density      = hash['Hsp_density'].to_i
+      hsp.qseq         = hash['Hsp_qseq']
+      hsp.hseq         = hash['Hsp_hseq']
+      hsp.midline      = hash['Hsp_midline']
+    end
+
+    def xmlparser_parse_statistics(hash)
+      labels = {
+        'db-num'	=> 'Statistics_db-num',
+        'db-len'	=> 'Statistics_db-len',
+        'hsp-len'	=> 'Statistics_hsp-len',
+        'eff-space'	=> 'Statistics_eff-space',
+        'kappa'	=> 'Statistics_kappa',
+        'lambda'	=> 'Statistics_lambda',
+        'entropy'	=> 'Statistics_entropy'
+      }
+      labels.each do |k,v|
+        case k
+        when 'db-num', 'db-len', 'hsp-len'
+          @iterations.last.statistics[k] = hash[v].to_i
+        else
+          @iterations.last.statistics[k] = hash[v].to_f
+        end
+      end
+    end
+        
+  end # class Report
+end # class Blast
+end # module Bio
+
+
+=begin
+
+This file is automatically loaded by bio/appl/blast/report.rb
+
+=end

data/lib/bio/appl/blat/report.rb

@@ -0,0 +1,489 @@
+#
+# = bio/appl/blat/report.rb - BLAT result parser
+#
+# Copyright:: Copyright (C) 2004 GOTO Naohisa <ng@bioruby.org>
+# License:: The Ruby License
+#
+#  $Id: report.rb,v 1.13 2007/04/05 23:35:39 trevor Exp $
+#
+# BLAT result parser (psl / pslx format).
+#
+# == Important Notes
+#
+# In BLAT results, the start position of a sequnece is numbered as 0.
+# On the other hand, in many other homology search programs,
+# the start position of a sequence is numbered as 1.
+# To keep compatibility, the BLAT parser adds 1 to every position number.
+#
+# == References
+#
+# * Kent, W.J., BLAT--the BLAST-like alignment tool,
+#   Genome Research, 12, 656--664, 2002.
+#   http://www.genome.org/cgi/content/abstract/12/4/656
+# * http://genome.ucsc.edu/goldenPath/help/blatSpec.html
+
+require 'bio'
+
+module Bio
+  class Blat
+
+    # Bio::Blat::Report is a BLAT report parser class.
+    # Its object may contain some Bio::Blat::Report::Hits objects.
+    #
+    # In BLAT results, the start position of a sequnece is numbered as 0.
+    # On the other hand, in many other homology search programs,
+    # the start position of a sequence is numbered as 1.
+    # To keep compatibility, the BLAT parser adds 1 to every position number
+    # except Bio::Blat::Report::Seqdesc and some Bio::Blat specific methods.
+    #
+    # Note that Bio::Blat::Report#query_def, #query_id, #query_len  methods
+    # simply return first hit's query_*.
+    # If multiple query sequences are given, these values
+    # will be incorrect.
+    #
+    class Report #< DB
+      # Delimiter of each entry. Bio::FlatFile uses it.
+      # In Bio::Blat::Report, it it nil (1 entry 1 file).
+      DELIMITER = RS = nil # 1 file 1 entry
+
+      # Creates a new Bio::Blat::Report object from BLAT result text (String).
+      # You can use Bio::FlatFile to read a file.
+      # Currently, results created with options -out=psl (default) or
+      # -out=pslx are supported.
+      def initialize(text)
+        flag = false
+        head = []
+        @hits = []
+        text.each do |line|
+          if flag then
+            @hits << Hit.new(line)
+          else
+            # for headerless data
+            if /^\d/ =~ line then
+              flag = true
+              redo
+            end
+            line = line.chomp
+            if /\A\-+\s*\z/ =~ line
+              flag = true
+            else
+              head << line
+            end
+          end
+        end
+        @columns = parse_header(head)
+      end
+
+      # hits of the result.
+      # Returns an Array of Bio::Blat::Report::Hit objects.
+      attr_reader :hits
+
+      # Returns descriptions of columns.
+      # Returns an Array.
+      # This would be a Bio::Blat specific method.
+      attr_reader :columns
+
+      # Parses headers.
+      def parse_header(ary)
+        while x = ary.shift
+          if /psLayout version (\S+)/ =~ x then
+            @psl_version = $1
+            break
+          elsif !(x.strip.empty?)
+            ary.unshift(x)
+            break
+          end
+        end
+        a0 = ary.collect { |x| x.split(/\t/) }
+        k = []
+        a0.each do |x|
+          x.each_index do |i|
+            y = x[i].strip
+            k[i] = k[i].to_s + (y.sub!(/\-\z/, '') ? y : y + ' ')
+          end
+        end
+        k.each { |x| x.strip! }
+        k
+      end
+      private :parse_header
+
+      # version of the psl format (String or nil).
+      attr_reader :psl_version
+
+      # Bio::Blat::Report::SeqDesc stores sequence information of
+      # query or subject of the BLAT report.
+      # It also includes some hit information.
+      class SeqDesc
+        # Creates a new SeqDesc object.
+        # It is designed to be called internally from Bio::Blat::Report class.
+        # Users shall not use it directly.
+        def initialize(gap_count, gap_bases, name, size,
+                       st, ed, starts, seqs)
+          @gap_count = gap_count.to_i
+          @gap_bases = gap_bases.to_i
+          @name = name
+          @size = size.to_i
+          @start = st.to_i
+          @end = ed.to_i
+          @starts = starts.collect { |x| x.to_i }
+          @seqs = seqs
+        end
+        # gap count
+        attr_reader :gap_count
+        # gap bases
+        attr_reader :gap_bases
+        # name of the sequence
+        attr_reader :name
+        # length of the sequence
+        attr_reader :size
+        # start position of the first segment
+        attr_reader :start
+        # end position of the final segment
+        attr_reader :end
+        # start positions of segments.
+        # Returns an array of numbers.
+        attr_reader :starts
+        # sequences of segments.
+        # Returns an array of String.
+        # Returns nil if there are no sequence data.
+        attr_reader :seqs
+      end #class SeqDesc
+
+      # Sequence segment pair of BLAT result.
+      # Similar to Bio::Blast::Report::Hsp but lacks many methods.
+      class SegmentPair
+        # Creates a new SegmentPair object.
+        # It is designed to be called internally from Bio::Blat::Report class.
+        # Users shall not use it directly.
+        def initialize(query_len, target_len, strand,
+                       blksize, qstart, tstart, qseq, tseq,
+                       protein_flag)
+          @blocksize  = blksize
+          @qseq       = qseq
+          @hseq       = hseq
+          @hit_strand   = 'plus'
+          w = (protein_flag ? 3 : 1) # 3 means query=protein target=dna
+          case strand
+          when '-'
+            # query is minus strand
+            @query_strand = 'minus'
+            # convert positions
+            @query_from = query_len - qstart
+            @query_to   = query_len - qstart - blksize + 1
+            # To keep compatibility, with other homology search programs,
+            # we add 1 to each position number.
+            @hit_from   = tstart + 1
+            @hit_to     = tstart + blksize * w # - 1 + 1
+          when '+-'
+            # hit is minus strand
+            @query_strand = 'plus'
+            @hit_strand = 'minus'
+            # To keep compatibility, with other homology search programs,
+            # we add 1 to each position number.
+            @query_from   = qstart + 1
+            @query_to     = qstart + blksize # - 1 + 1
+            # convert positions
+            @hit_from     = target_len - tstart
+            @hit_to       = target_len - tstart - blksize * w + 1
+          else #when '+', '++'
+            @query_strand = 'plus'
+            # To keep compatibility with other homology search programs,
+            # we add 1 to each position number.
+            @query_from = qstart + 1
+            @query_to   = qstart + blksize # - 1 + 1
+            @hit_from   = tstart + 1
+            @hit_to     = tstart + blksize * w # - 1 + 1
+          end
+        end
+        # Returns query start position.
+        # CAUTION: In Blat's raw result(psl format), first position is 0.
+        # To keep compatibility, the parser add 1 to the position.
+        attr_reader :query_from
+
+        # Returns query end position.
+        # CAUTION: In Blat's raw result(psl format), first position is 0.
+        # To keep compatibility, the parser add 1 to the position.
+        attr_reader :query_to
+
+        # Returns query sequence.
+        # If sequence data is not available, returns nil.
+        attr_reader :qseq
+
+        # Returns strand information of the query.
+        # Returns 'plus' or 'minus'.
+        attr_reader :query_strand
+
+        # Returns target (subject, hit) start position.
+        # CAUTION: In Blat's raw result(psl format), first position is 0.
+        # To keep compatibility, the parser add 1 to the position.
+        attr_reader :hit_from
+
+        # Returns target (subject, hit) end position.
+        # CAUTION: In Blat's raw result(psl format), first position is 0.
+        # To keep compatibility, the parser add 1 to the position.
+        attr_reader :hit_to
+
+        # Returns the target (subject, hit) sequence.
+        # If sequence data is not available, returns nil.
+        attr_reader :hseq
+
+        # Returns strand information of the target (subject, hit).
+        # Returns 'plus' or 'minus'.
+        attr_reader :hit_strand
+
+        # Returns block size (length) of the segment pair.
+        # This would be a Bio::Blat specific method.
+       attr_reader :blocksize
+
+        # Returns alignment length of the segment pair.
+        # Returns nil if no alignment data are available.
+        def align_len
+          @qseq ? @qseq.size : nil
+        end
+      end #class SegmentPair
+
+      # Hit class for the BLAT result parser.
+      # Similar to Bio::Blast::Report::Hit but lacks many methods.
+      # Its object may contain some Bio::Blat::Report::SegmentPair objects.
+      class Hit
+        # Creates a new Hit object from a piece of BLAT result text.
+        # It is designed to be called internally from Bio::Blat::Report object.
+        # Users shall not use it directly.
+        def initialize(str)
+          @data = str.chomp.split(/\t/)
+        end
+
+        # Raw data of the hit.
+        # (Note that it doesn't add 1 to position numbers.)
+        attr_reader :data
+
+        # split comma-separeted text
+        def split_comma(str)
+          str.to_s.sub(/\s*\,+\s*\z/, '').split(/\s*\,\s*/)
+        end
+        private :split_comma
+
+        # Returns sequence informations of the query.
+        # Returns a Bio::Blat::Report::SeqDesc object.
+        # This would be Bio::Blat specific method.
+        def query
+          unless defined?(@query)
+            d = @data
+            @query = SeqDesc.new(d[4], d[5], d[9], d[10], d[11], d[12],
+                                 split_comma(d[19]), split_comma(d[21]))
+          end
+          @query
+        end
+
+        # Returns sequence informations of the target(hit).
+        # Returns a Bio::Blat::Report::SeqDesc object.
+        # This would be Bio::Blat specific method.
+        def target
+          unless defined?(@target)
+            d = @data
+            @target = SeqDesc.new(d[6], d[7], d[13], d[14], d[15], d[16],
+                                  split_comma(d[20]), split_comma(d[22]))
+          end
+          @target
+        end
+
+        # Match nucleotides.
+        def match;       @data[0].to_i;  end
+        # Mismatch nucleotides.
+        def mismatch;    @data[1].to_i;  end
+
+        # "rep. match".
+        # Number of bases that match but are part of repeats.
+        # Note that current version of BLAT always set 0.
+        def rep_match;   @data[2].to_i;  end
+
+        # "N's". Number of 'N' bases.
+        def n_s;         @data[3].to_i;  end
+
+        # Returns strand information of the hit.
+        # Returns '+' or '-'.
+        # This would be a Bio::Blat specific method.
+        def strand;      @data[8];       end
+
+        # Number of blocks(exons, segment pairs).
+        def block_count; @data[17].to_i; end
+
+        # Sizes of all blocks(exons, segment pairs).
+        # Returns an array of numbers.
+        def block_sizes
+          unless defined?(@block_sizes) then
+            @block_sizes = split_comma(@data[18]).collect { |x| x.to_i }
+          end
+          @block_sizes
+        end
+
+        # Returns blocks(exons, segment pairs) of the hit.
+        # Returns an array of Bio::Blat::Report::SegmentPair objects.
+        def blocks
+          unless defined?(@blocks)
+            bs    = block_sizes
+            qst   = query.starts
+            tst   = target.starts
+            qseqs = query.seqs
+            tseqs = target.seqs
+            pflag = self.protein?
+            @blocks = (0...block_count).collect do |i|
+              SegmentPair.new(query.size, target.size, strand, bs[i],
+                              qst[i], tst[i], qseqs[i], tseqs[i],
+                              pflag)
+            end
+          end
+          @blocks
+        end
+        alias exons blocks
+
+        #--
+        # Bio::BLAST::*::Report::Hit compatible methods
+        #++
+        alias hsps blocks
+
+        # Returns the length of query sequence.
+        def query_len;  query.size;  end
+
+        # Returns the name of query sequence.
+        def query_def;  query.name;  end
+        alias query_id query_def
+
+        # Returns the length of the target(subject) sequence.
+        def target_len; target.size; end
+        alias len target_len
+
+        # Returns the name of the target(subject) sequence.
+        def target_def; target.name; end
+        alias target_id target_def
+        alias definition target_def
+
+        #Iterates over each block(exon, segment pair) of the hit.
+        # Yields a Bio::Blat::Report::SegmentPair object.
+        def each(&x) #:yields: segmentpair
+          exons.each(&x)
+        end
+
+        #--
+        # methods described in the BLAT FAQ at the UCSC genome browser.
+        # (http://genome.ucsc.edu/FAQ/FAQblat#blat4)
+        #++
+
+        # Calculates the pslCalcMilliBad value defined in the
+        # BLAT FAQ (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
+        #
+        # The algorithm is taken from the BLAT FAQ
+        # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
+        def milli_bad
+          w = (self.protein? ? 3 : 1)
+          qalen = w * (self.query.end - self.query.start)
+          talen = self.target.end - self.target.start
+          alen = (if qalen < talen then qalen; else talen; end)
+          return 0 if alen <= 0
+          d = qalen - talen
+          d = 0 if d < 0
+          total = w * (self.match + self.rep_match + self.mismatch)
+          return 0 if total == 0
+          return (1000 * (self.mismatch * w + self.query.gap_count +
+                            (3 * Math.log(1 + d)).round) / total)
+        end
+
+        # Calculates the percent identity compatible with the BLAT web server
+        # as described in the BLAT FAQ
+        # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
+        #
+        # The algorithm is taken from the BLAT FAQ
+        # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
+        def percent_identity
+          100.0 - self.milli_bad * 0.1
+        end
+
+        # When the output data comes from the protein query, returns true.
+        # Otherwise (nucleotide query), returns false.
+        # It returns nil if this cannot be determined.
+        #
+        # The algorithm is taken from the BLAT FAQ
+        # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
+        #
+        # Note: It seems that it returns true only when protein query
+        # with nucleotide database (blat options: -q=prot -t=dnax).
+        def protein?
+          return nil if self.block_sizes.empty?
+          case self.strand[1,1]
+          when '+'
+            if self.target.end == self.target.starts[-1] +
+                3 * self.block_sizes[-1] then
+              true
+            else
+              false
+            end
+          when '-'
+            if self.target.start == self.target.size -
+                self.target.starts[-1] - 3 * self.block_sizes[-1] then
+              true
+            else
+              false
+            end
+          else
+            nil
+          end
+        end
+
+        # Calculates the score compatible with the BLAT web server
+        # as described in the BLAT FAQ
+        # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
+        #
+        # The algorithm is taken from the BLAT FAQ
+        # (http://genome.ucsc.edu/FAQ/FAQblat#blat4).
+        def score
+          w = (self.protein? ? 3 : 1)
+          w * (self.match + (self.rep_match >> 1)) -
+            w * self.mismatch - self.query.gap_count - self.target.gap_count
+        end
+      end #class Hit
+
+      #--
+      #Bio::BLAST::*::Report compatible methods
+      #++
+
+      # Returns number of hits.
+      # Same as hits.size.
+      def num_hits;     @hits.size;     end
+
+      # Iterates over each Bio::Blat::Report::Hit object.
+      # Same as hits.each.
+      def each_hit(&x) #:yields: hit
+        @hits.each(&x)
+      end
+      alias each each_hit
+
+      # Returns the name of query sequence.
+      # CAUTION: query_* methods simply return first hit's query_*.
+      # If multiple query sequences are given, these values
+      # will be incorrect.
+      def query_def; (x = @hits.first) ? x.query_def : nil; end
+
+      # Returns the length of query sequence.
+      # CAUTION: query_* methods simply return first hit's query_*.
+      # If multiple query sequences are given, these values
+      # will be incorrect.
+      def query_len; (x = @hits.first) ? x.query_len : nil; end
+      alias query_id query_def
+    end #class Report
+
+  end #class Blat
+end #module Bio
+
+=begin
+
+= Bio::Blat::Report
+
+  BLAT result parser. (psl / pslx format)
+
+= References
+
+* ((<URL:http://www.genome.org/cgi/content/abstract/12/4/656>))
+  Kent, W.J., BLAT--the BLAST-like alignment tool,
+  Genome Research, 12, 656--664, 2002.
+
+=end