bio 0.7.0

data/lib/bio/appl/hmmer.rb

@@ -0,0 +1,129 @@
+#
+# bio/appl/hmmer.rb - HMMER wrapper
+# 
+#   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: hmmer.rb,v 1.4 2005/09/26 13:00:04 k Exp $
+#
+
+require 'bio/command'
+require 'shellwords'
+
+module Bio
+
+  class HMMER
+
+    autoload :Report, 'bio/appl/hmmer/report'
+
+    include Bio::Command::Tools
+
+    def initialize(program, hmmfile, seqfile, opt = [])
+      @program	= program
+      @hmmfile	= hmmfile
+      @seqfile	= seqfile
+      @output	= ''
+
+      begin
+        @options = opt.to_ary
+      rescue NameError #NoMethodError
+        # backward compatibility
+        @options = Shellwords.shellwords(opt)
+      end
+    end
+    attr_accessor :program, :hmmfile, :seqfile, :options
+    attr_reader :output
+
+    def option
+      # backward compatibility
+      make_command_line(@options)
+    end
+
+    def option=(str)
+      # backward compatibility
+      @options = Shellwords.shellwords(str)
+    end
+
+    def query
+      cmd = [ @program, *@options ]
+      cmd.concat([ @hmmfile, @seqfile ])
+      
+      report = nil
+
+      @output = call_command_local(cmd, nil)
+      report = parse_result(@output)
+      
+      return report
+    end
+
+
+    private
+
+    def parse_result(data)
+      Report.new(data)
+    end
+
+  end
+end
+
+
+
+if __FILE__ == $0
+
+  begin
+    require 'pp'
+    alias p pp
+  rescue
+  end
+
+  program = ARGV.shift	# hmmsearch, hmmpfam
+  hmmfile = ARGV.shift
+  seqfile = ARGV.shift
+
+  factory = Bio::HMMER.new(program, hmmfile, seqfile)
+  p factory.query
+
+end
+
+
+=begin
+
+= Bio::HMMER
+
+--- Bio::HMMER.new(program, hmmfile, seqfile, option = '')
+--- Bio::HMMER#program
+--- Bio::HMMER#hmmfile
+--- Bio::HMMER#seqfile
+--- Bio::HMMER#options
+
+      Accessors for the factory.
+
+--- Bio::HMMER#option
+--- Bio::HMMER#option=(str)
+
+      Get/set options by string.
+
+--- Bio::HMMER#query
+
+      Executes the hmmer search and returns Report object (Bio::HMMER::Report).
+
+--- Bio::HMMER#output
+
+      Shows the raw output from hmmer search.
+
+=end
+
+

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

@@ -0,0 +1,556 @@
+#
+# bio/appl/hmmer/report.rb - hmmsearch, hmmpfam parserer
+#
+#   Copyright (C) 2002 Hiroshi Suga <suga@biophys.kyoto-u.ac.jp>
+#   Copyright (C) 2005 Masashi Fujita <fujita@kuicr.kyoto-u.ac.jp>
+#
+#  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: report.rb,v 1.9 2005/10/31 09:12:03 k Exp $
+#
+
+require 'bio/appl/hmmer'
+
+module Bio
+  class HMMER
+
+    def self.reports(input)
+      ary = []
+      input.each("\n//\n") do |data|
+        if block_given?
+          yield Report.new(data)
+        else
+          ary << Report.new(data)
+        end
+      end
+      return ary
+    end
+
+
+    # Bio::HMMER::Report
+    class Report
+
+      # for Bio::FlatFile support
+      DELIMITER = RS = "\n//\n"
+
+      def initialize(data)
+
+        # The input data is divided into six data fields, i.e. header,
+        # query infomation, hits, HSPs, alignments and search statistics.
+        # However, header and statistics data don't necessarily exist.
+        subdata, is_hmmsearch = get_subdata(data)
+
+        # if header exists, parse it
+        if subdata["header"]
+          @program, @parameter = parse_header_data(subdata["header"])
+        else
+          @program, @parameter = [{}, {}]
+        end
+
+        @query_info = parse_query_info(subdata["query"])
+        @hits       = parse_hit_data(subdata["hit"])
+        @hsps       = parse_hsp_data(subdata["hsp"], is_hmmsearch)
+
+        if @hsps != []
+          # split alignment subdata into an array of alignments
+          aln_ary = subdata["alignment"].split(/^\S+.*?\n/).slice(1..-1)
+
+          # append alignment information to corresponding Hsp
+          aln_ary.each_with_index do |aln, i|
+            @hsps[i].set_alignment(aln)
+          end
+        end
+
+        # assign each Hsp object to its parent Hit
+        hits_hash = {}
+        @hits.each do |hit|
+          hits_hash[hit.accession] = hit
+        end
+        @hsps.each do |hsp|
+          if hits_hash.has_key?(hsp.accession)
+            hits_hash[hsp.accession].append_hsp(hsp)
+          end
+        end
+
+        # parse statistics (for hmmsearch)
+        if is_hmmsearch
+          @histogram, @statistical_detail, @total_seq_searched, \
+          @whole_seq_top_hits, @domain_top_hits = \
+          parse_stat_data(subdata["statistics"])
+        end
+
+      end
+      attr_reader :program, :parameter, :query_info, :hits, :hsps,
+        :histogram, :statistical_detail, :total_seq_searched,
+        :whole_seq_top_hits, :domain_top_hits
+
+
+      def each
+        @hits.each do |x|
+          yield x
+        end
+      end
+
+
+      # Bio::HMMER::Report::Hit
+      class Hit
+        def initialize(data)
+          @hsps = Array.new
+          if /^(\S+)\s+(.*?)\s+(\S+)\s+(\S+)\s+(\S+)$/ =~ data
+            @accession, @description, @score, @evalue, @num = 
+              [$1, $2, $3.to_f, $4.to_f, $5.to_i]
+          end
+        end
+        attr_reader :hsps, :accession, :description, :score, :evalue, :num
+
+        def each
+          @hsps.each do |x|
+            yield x
+          end
+        end
+
+        alias target_id  accession
+        alias hit_id     accession
+        alias entry_id   accession
+        alias definition description
+        alias bit_score  score
+
+        def target_def
+          if @hsps.size == 1
+            "<#{@hsps[0].domain}> #{@description}"
+          else
+            "<#{@num.to_s}> #{@description}"
+          end
+        end
+
+        def append_hsp(hsp)
+          @hsps << hsp
+        end
+
+      end
+
+
+      # Bio::HMMER::Report::Hsp
+      class Hsp
+        def initialize(data, is_hmmsearch)
+          @is_hmmsearch = is_hmmsearch
+
+          @accession, @domain, seq_f, seq_t, @seq_ft, hmm_f, hmm_t, @hmm_ft,
+            score, evalue = data.split(' ')
+          @seq_f = seq_f.to_i
+          @seq_t = seq_t.to_i
+          @hmm_f = hmm_f.to_i
+          @hmm_t = hmm_t.to_i
+          @score = score.to_f
+          @evalue = evalue.to_f
+          @hmmseq = ''
+          @flatseq = ''
+          @midline = ''
+          @query_frame = 1
+          @target_frame = 1
+          # CS and RF lines are rarely used.
+          @csline = nil
+          @rfline = nil
+        end
+        attr_reader :accession, :domain, :seq_f, :seq_t, :seq_ft,
+          :hmm_f, :hmm_t, :hmm_ft, :score, :evalue, :midline, :hmmseq,
+          :flatseq, :query_frame, :target_frame, :csline, :rfline
+
+        def set_alignment(aln)
+          # First, split the input alignment into an array of
+          # "alignment blocks." One block usually has three lines,
+          # i.e. hmmseq, midline and flatseq. 
+          # However, although infrequent, it can contain CS or RF lines.
+          aln.split(/ (?:\d+|-)\s*\n\n/).each do |blk|
+            lines = blk.split(/\n/)   
+            cstmp = (lines[0] =~ /^ {16}CS/) ? lines.shift : nil
+            rftmp = (lines[0] =~ /^ {16}RF/) ? lines.shift : nil
+            aln_width = lines[0][/\S+/].length
+            @csline  = @csline.to_s + cstmp[19, aln_width] if cstmp
+            @rfline  = @rfline.to_s + rftmp[19, aln_width] if rftmp
+            @hmmseq  += lines[0][19, aln_width]
+            @midline += lines[1][19, aln_width]
+            @flatseq += lines[2][19, aln_width]
+          end
+          @csline  = @csline[3...-3] if @csline
+          @rfline  = @rfline[3...-3] if @rfline
+          @hmmseq  = @hmmseq[3...-3]
+          @midline = @midline[3...-3]
+          @flatseq = @flatseq[3...-3]
+        end
+
+        def query_seq;   @is_hmmsearch ? @hmmseq  : @flatseq; end
+        def target_seq;  @is_hmmsearch ? @flatseq : @hmmseq;  end
+        def target_from; @is_hmmsearch ? @seq_f   : @hmm_f;   end
+        def target_to;   @is_hmmsearch ? @seq_t   : @hmm_t;   end
+        def query_from;  @is_hmmsearch ? @hmm_f   : @seq_f;   end
+        def query_to;    @is_hmmsearch ? @hmm_t   : @seq_t;   end
+
+        alias bit_score score
+        alias target_id accession
+
+      end
+
+
+      # Bio::HMMER::Report#get_subdata
+      def get_subdata(data)
+        subdata = {}
+        header_prefix = '\Ahmm(search|pfam) - search'
+        query_prefix  = '^Query (HMM|sequence): .*\nAccession: '
+        hit_prefix    = '^Scores for (complete sequences|sequence family)'
+        hsp_prefix    = '^Parsed for domains:'
+        aln_prefix    = '^Alignments of top-scoring domains:\n'
+        stat_prefix   = '^\nHistogram of all scores:'
+
+        # if header exists, get it
+        if data =~ /#{header_prefix}/
+          is_hmmsearch = ($1 == "search")   # hmmsearch or hmmpfam
+          subdata["header"] = data[/(\A.+?)(?=#{query_prefix})/m]
+        else
+          is_hmmsearch = false   # if no header, assumed to be hmmpfam
+        end
+
+        # get query, Hit and Hsp data
+        subdata["query"] = data[/(#{query_prefix}.+?)(?=#{hit_prefix})/m]
+        subdata["hit"]   = data[/(#{hit_prefix}.+?)(?=#{hsp_prefix})/m]
+        subdata["hsp"]   = data[/(#{hsp_prefix}.+?)(?=#{aln_prefix})/m]
+
+        # get alignment data
+        if is_hmmsearch
+          data =~ /#{aln_prefix}(.+?)#{stat_prefix}/m
+          subdata["alignment"] = $1
+        else
+          data =~ /#{aln_prefix}(.+?)\/\/\n/m
+          subdata["alignment"] = $1
+          raise "multiple reports found" if $'.length > 0
+        end
+
+        # handle -A option of HMMER
+        cutoff_line = '\t\[output cut off at A = \d+ top alignments\]\n\z'
+        subdata["alignment"].sub!(/#{cutoff_line}/, '')
+
+        # get statistics data
+        subdata["statistics"] = data[/(#{stat_prefix}.+)\z/m]
+
+        [subdata, is_hmmsearch]
+      end
+      private :get_subdata
+      
+      # Bio::HMMER::Report#parse_header_data
+      def parse_header_data(data)
+        data =~ /\A(.+? - - -$\n)(.+? - - -$\n)\n\z/m
+        program_data   = $1
+        parameter_data = $2
+
+        program = {}
+        program['name'], program['version'], program['copyright'], \
+        program['license'] = program_data.split(/\n/)
+
+        parameter = {}
+        parameter_data.each do |x|
+          if /^(.+?):\s+(.*?)\s*$/ =~ x
+            parameter[$1] = $2
+          end
+        end
+
+        [program, parameter]
+      end
+      private :parse_header_data
+
+      # Bio::HMMER::Report#parse_query_info
+      def parse_query_info(data)
+        hash = {}
+        data.each do |x|
+          if /^(.+?):\s+(.*?)\s*$/ =~ x
+            hash[$1] = $2
+          elsif /\s+\[(.+)\]/ =~ x
+            hash['comments'] = $1
+          end
+        end
+        hash
+      end
+      private :parse_query_info
+
+      # Bio::HMMER::Report#parse_hit_data
+      def parse_hit_data(data)
+        data.sub!(/.+?---\n/m, '').chop!
+        hits = []
+        return hits if data == "\t[no hits above thresholds]\n"
+        data.each do |l|
+          hits.push(Hit.new(l))
+        end
+        hits
+      end
+      private :parse_hit_data
+
+      # Bio::HMMER::Report#parse_hsp_data
+      def parse_hsp_data(data, is_hmmsearch)
+        data.sub!(/.+?---\n/m, '').chop!
+        hsps=[]
+        return hsps if data == "\t[no hits above thresholds]\n"
+        data.each do |l|
+          hsps.push(Hsp.new(l, is_hmmsearch))
+        end
+        return hsps
+      end
+      private :parse_hsp_data
+
+      # Bio::HMMER::Report#parse_stat_data
+      def parse_stat_data(data)
+        data.sub!(/\nHistogram of all scores:\n(.+?)\n\n\n%/m, '')
+        histogram = $1
+
+        statistical_detail = {}
+        data.sub!(/(.+?)\n\n/m, '')
+        $1.each do |l|
+          statistical_detail[$1] = $2.to_f if /^\s*(.+?)\s*=\s*(\S+)/ =~ l
+        end
+        
+        total_seq_searched = nil
+        data.sub!(/(.+?)\n\n/m, '')
+        $1.each do |l|
+          total_seq_searched = $2.to_i if /^\s*(.+)\s*:\s*(\S+)/ =~ l
+        end
+        
+        whole_seq_top_hits = {}
+        data.sub!(/(.+?)\n\n/m, '')
+        $1.each do |l|
+          if /^\s*(.+?):\s*(\d+)\s*$/ =~ l
+            whole_seq_top_hits[$1] = $2.to_i
+          elsif /^\s*(.+?):\s*(\S+)\s*$/ =~ l
+            whole_seq_top_hits[$1] = $2
+          end
+        end
+        
+        domain_top_hits = {}
+        data.each do |l|
+          if /^\s*(.+?):\s*(\d+)\s*$/ =~ l
+            domain_top_hits[$1] = $2.to_i
+          elsif /^\s*(.+?):\s*(\S+)\s*$/ =~ l
+            domain_top_hits[$1] = $2
+          end
+        end
+
+        [histogram, statistical_detail, total_seq_searched, \
+          whole_seq_top_hits, domain_top_hits]
+      end
+      private :parse_stat_data
+
+    end
+
+  end
+end
+
+
+if __FILE__ == $0
+
+=begin
+
+  #
+  # for multiple reports in a single output file (hmmpfam)
+  #
+  Bio::HMMER.reports(ARGF.read) do |report|
+    report.hits.each do |hit|
+      hit.hsps.each do |hsp|
+      end
+    end
+  end
+
+=end
+
+  begin
+    require 'pp'
+    alias p pp
+  rescue LoadError
+  end
+
+  rep = Bio::HMMER::Report.new(ARGF.read)
+  p rep
+
+  indent = 18
+
+  puts "### hmmer result"
+  print "name : ".rjust(indent)
+  p  rep.program['name']
+  print "version : ".rjust(indent)
+  p rep.program['version']
+  print "copyright : ".rjust(indent)
+  p rep.program['copyright']
+  print "license : ".rjust(indent)
+  p rep.program['license']
+
+  print "HMM file : ".rjust(indent)
+  p rep.parameter['HMM file']
+  print "Sequence file : ".rjust(indent)
+  p rep.parameter['Sequence file']
+
+  print "Query sequence : ".rjust(indent)
+  p rep.query_info['Query sequence']
+  print "Accession : ".rjust(indent)
+  p rep.query_info['Accession']
+  print "Description : ".rjust(indent)
+  p rep.query_info['Description']
+
+  rep.each do |hit|
+    puts "## each hit"
+    print "accession : ".rjust(indent)
+    p [ hit.accession, hit.target_id, hit.hit_id, hit.entry_id ]
+    print "description : ".rjust(indent)
+    p [ hit.description, hit.definition ]
+    print "target_def : ".rjust(indent)
+    p hit.target_def
+    print "score : ".rjust(indent)
+    p [ hit.score, hit.bit_score ]
+    print "evalue : ".rjust(indent)
+    p hit.evalue
+    print "num : ".rjust(indent)
+    p hit.num
+
+    hit.each do |hsp|
+      puts "## each hsp"
+      print "accession : ".rjust(indent)
+      p [ hsp.accession, hsp.target_id ]
+      print "domain : ".rjust(indent)
+      p hsp.domain
+      print "seq_f : ".rjust(indent)
+      p hsp.seq_f
+      print "seq_t : ".rjust(indent)
+      p hsp.seq_t
+      print "seq_ft : ".rjust(indent)
+      p hsp.seq_ft
+      print "hmm_f : ".rjust(indent)
+      p hsp.hmm_f
+      print "hmm_t : ".rjust(indent)
+      p hsp.hmm_t
+      print "hmm_ft : ".rjust(indent)
+      p hsp.hmm_ft
+      print "score : ".rjust(indent)
+      p [ hsp.score, hsp.bit_score ]
+      print "evalue : ".rjust(indent)
+      p hsp.evalue
+      print "midline : ".rjust(indent)
+      p hsp.midline
+      print "hmmseq : ".rjust(indent)
+      p hsp.hmmseq
+      print "flatseq : ".rjust(indent)
+      p hsp.flatseq
+      print "query_frame : ".rjust(indent)
+      p hsp.query_frame
+      print "target_frame : ".rjust(indent)
+      p hsp.target_frame
+
+      print "query_seq : ".rjust(indent)
+      p hsp.query_seq		# hmmseq, flatseq
+      print "target_seq : ".rjust(indent)
+      p hsp.target_seq		# flatseq, hmmseq
+      print "target_from : ".rjust(indent)
+      p hsp.target_from		# seq_f, hmm_f
+      print "target_to : ".rjust(indent)
+      p hsp.target_to		# seq_t, hmm_t
+      print "query_from : ".rjust(indent)
+      p hsp.query_from		# hmm_f, seq_f
+      print "query_to : ".rjust(indent)
+      p hsp.query_to		# hmm_t, seq_t
+    end
+  end
+
+end
+
+
+=begin
+
+= Bio::HMMER::Report
+
+--- Bio::HMMER::Report.new(data)
+--- Bio::HMMER::Report#each
+
+      Iterates on each Bio::HMMER::Report::Hit object.
+
+--- Bio::HMMER::Report#hits
+
+      Returns an Array of Bio::HMMER::Report::Hit objects.
+
+
+== Bio::HMMER::Report::Hit
+
+--- Bio::HMMER::Report::Hit#each
+
+      Iterates on each Hsp object.
+
+--- Bio::HMMER::Report::Hit#hsps
+
+      Returns an Array of Bio::HMMER::Report::Hsp objects.
+
+--- Bio::HMMER::Report::Hit#target_id
+--- Bio::HMMER::Report::Hit#hit_id
+--- Bio::HMMER::Report::Hit#entry_id
+--- Bio::HMMER::Report::Hit#definition
+--- Bio::HMMER::Report::Hit#description
+--- Bio::HMMER::Report::Hit#num
+
+      nunmer of domains
+
+--- Bio::HMMER::Report::Hit#target_def
+
+      <domain number> + @description
+
+--- Bio::HMMER::Report::Hit#evalue
+--- Bio::HMMER::Report::Hit#bit_score
+--- Bio::HMMER::Report::Hit#score
+
+      Matching scores (total of all HSPs).
+
+
+== Bio::HMMER::Report::Hsp
+
+--- Bio::HMMER::Report#hsps
+
+      Returns an Array of Bio::HMMER::Report::Hsp objects.
+      Under special circumstances, some HSPs do not have
+      parent Hit objects. If you want to access such HSPs,
+      use this method.
+
+--- Bio::HMMER::Report::Hsp#target_id
+--- Bio::HMMER::Report::Hsp#accession
+--- Bio::HMMER::Report::Hsp#domain
+--- Bio::HMMER::Report::Hsp#seq_f
+--- Bio::HMMER::Report::Hsp#seq_t
+--- Bio::HMMER::Report::Hsp#seq_ft
+--- Bio::HMMER::Report::Hsp#hmm_f
+--- Bio::HMMER::Report::Hsp#hmm_t
+--- Bio::HMMER::Report::Hsp#hmm_ft
+
+--- Bio::HMMER::Report::Hsp#bit_score
+--- Bio::HMMER::Report::Hsp#score
+--- Bio::HMMER::Report::Hsp#evalue
+
+--- Bio::HMMER::Report::Hsp#midline
+--- Bio::HMMER::Report::Hsp#hmmseq
+--- Bio::HMMER::Report::Hsp#flatseq
+--- Bio::HMMER::Report::Hsp#query_frame
+--- Bio::HMMER::Report::Hsp#target_frame
+
+--- Bio::HMMER::Report::Hsp#query_seq
+--- Bio::HMMER::Report::Hsp#query_from
+--- Bio::HMMER::Report::Hsp#query_to
+--- Bio::HMMER::Report::Hsp#target_seq
+--- Bio::HMMER::Report::Hsp#target_from
+--- Bio::HMMER::Report::Hsp#target_to
+
+--- Bio::HMMER::Report::Hsp#csline
+--- Bio::HMMER::Report::Hsp#rfline
+
+=end
+