bio 0.7.0

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

@@ -0,0 +1,570 @@
+#
+# = bio/appl/genscan/report.rb - Genscan report classes
+#
+# Copyright::  Copyright (C) 2003 Mitsuteru C. Nakao <n@bioruby.org>
+# License::    LGPL
+#
+#  $Id: report.rb,v 1.8 2005/12/18 15:58:40 k Exp $
+#
+# == Description
+#
+#
+# == Example
+# == References
+#
+#--
+#
+#  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 1.8 2005/12/18 15:58:40 k Exp $
+#
+#++
+#
+
+require 'bio/db/fasta'
+
+
+module Bio
+
+# = Bio::Genscan
+class Genscan
+
+  # = Bio::Genscan::Report - Class for Genscan report output.
+  #
+  # Parser for the Genscan report output.
+  # * Genscan http://genes.mit.edu/GENSCAN.html
+  class Report
+
+    # Returns Genscan version.
+    attr_reader :genscan_version
+
+    # Returns
+    attr_reader :date_run
+
+    # Returns
+    attr_reader :time
+
+    # Returns Name of query sequence.
+    attr_reader :query_name
+    alias_method :sequence_name, :query_name
+    alias_method :name,          :query_name
+
+    # Returns Length of the query sequence.
+    attr_reader :length
+
+    # Returns C+G content of the query sequence.
+    attr_reader :gccontent
+
+    # Returns
+    attr_reader :isochore
+
+    # Returns
+    attr_reader :matrix
+
+    # Returns Array of Bio::Genscan::Report::Gene.
+    attr_reader :predictions
+    alias_method :prediction, :predictions
+    alias_method :genes,      :predictions
+
+
+    # Bio::Genscan::Report.new(str)
+    #
+    # Parse a Genscan report output string.
+    def initialize(report)
+      @predictions = []
+      @genscan_version = nil
+      @date_run   = nil
+      @time       = nil
+      @query_name = nil
+      @length     = nil
+      @gccontent  = nil
+      @isochore   = nil
+      @matrix     = nil
+
+      report.each("\n") do |line|
+        case line
+        when /^GENSCAN/
+          parse_headline(line)
+        when /^Sequence/
+          parse_sequence(line)
+        when /^Parameter/
+          parse_parameter(line)
+        when /^Predicted genes/
+          break
+        end
+      end
+
+      # rests
+      i = report.index(/^Predicted gene/)
+      j = report.index(/^Predicted peptide sequence/)
+
+      # genes/exons
+      genes_region = report[i...j]
+      genes_region.each("\n") do |line|
+        if /Init|Intr|Term|PlyA|Prom|Sngl/ =~ line
+          gn, en = line.strip.split(" +")[0].split(/\./).map {|i| i.to_i }
+          add_exon(gn, en, line)
+        end
+      end
+
+      # sequences (peptide|CDS)
+      sequence_region = report[j...report.size]
+      sequence_region.gsub!(/^Predicted .+?:/, '')
+      sequence_region.gsub!(/^\s*$/, '')
+      sequence_region.split(Bio::FastaFormat::RS).each do |ff|
+        add_seq(Bio::FastaFormat.new(ff))
+      end
+    end
+
+
+    # Bio::Genscan::Report#parse_headline
+    def parse_headline(line)
+      tmp = line.chomp.split(/\t/)
+      @genscan_version = tmp[0].split(' ')[1]
+      @date_run        = tmp[1].split(': ')[1]
+      @time            = tmp[2].split(': ')[1]
+    end
+    private :parse_headline
+
+
+    # Bio::Genscan::Report#parse_sequence
+    def parse_sequence(line)
+      if /^Sequence (\S+) : (\d+) bp : (\d+[\.\d]+)% C\+G : Isochore (\d+.+?)$/ =~ line
+        @query_name = $1
+        @length     = $2.to_i
+        @gccontent  = $3.to_f
+        @isochore   = $4
+      else
+        raise "Error: [#{line.inspect}]"
+      end
+    end
+    private :parse_sequence
+
+
+    # Bio::Genscan::Report#parse_parameter
+    def parse_parameter(line)
+      if /^Parameter matrix: (\w.+)$/ =~ line.chomp
+        @matrix = $1
+      else
+        raise "Error: [#{line}]"  
+      end
+    end
+    private :parse_parameter
+
+
+    # Bio::Genscan::Report#add_gene
+    def add_gene(gn)
+      @predictions[gn - 1] = Gene.new(gn)
+    end
+    private :add_gene
+    
+
+    # Bio::Genscan::Report#add_exon
+    def add_exon(gn, en, line)
+      exon = Exon.parser(line)
+      case line
+      when /Prom/
+        begin
+          @predictions[gn - 1].set_promoter(exon)
+        rescue NameError
+          add_gene(gn)
+          @predictions[gn - 1].set_promoter(exon)
+        end
+      when /PlyA/
+        @predictions[gn - 1].set_polyA(exon)
+      else
+        begin
+          @predictions[gn - 1].exons[en - 1] = exon
+        rescue NameError
+          add_gene(gn)
+          @predictions[gn - 1].exons[en - 1] = exon
+        end
+      end
+    end
+    private :add_exon
+      
+
+    # Bio::Genscan::Report#add_seq
+    def add_seq(seq)
+      if /peptide_(\d+)/ =~ seq.definition
+        gn = $1.to_i
+        @predictions[gn - 1].set_aaseq(seq)
+      elsif /CDS_(\d+)/ =~ seq.definition
+        gn = $1.to_i
+        @predictions[gn - 1].set_naseq(seq)
+      end
+    end
+    private :add_seq
+
+
+    # = Container class of predicted gene structures.
+    class Gene
+
+      # Bio::Genescan::Report::Gene.new(gene_number)
+      def initialize(gn)
+        @number = gn.to_i
+        @aaseq = Bio::FastaFormat.new("")
+        @naseq = Bio::FastaFormat.new("")
+        @promoter = nil
+        @exons    = []
+        @polyA    = nil
+      end
+
+      # Returns "Gn", gene number field.
+      attr_reader :number
+
+      # Returns Bio::FastaFormat object.
+      attr_reader :aaseq
+
+      # Returns Bio::FastaFormat object.
+      attr_reader :naseq
+
+      # Returns Array of Bio::Genscan::Report::Exon.
+      attr_reader :exons
+
+      # Returns Bio::Genscan::Report::Exon object.
+      attr_reader :promoter
+
+      # Returns Bio::Genscan::Report::Exon object.
+      attr_reader :polyA
+
+
+      # Bio::Genescan::Report::Gene#seq_aaseq
+      def set_aaseq(seq)
+        @aaseq = seq
+      end
+
+        
+      # Bio::Genescan::Report::Gene#seq_naseq
+      def set_naseq(seq)
+        @naseq = seq
+      end
+
+
+      # Bio::Genescan::Report::Gene#seq_promoter
+      def set_promoter(segment)
+        @promoter = segment
+      end
+
+
+      # Bio::Genescan::Report::Gene#seq_polyA
+      def set_polyA(segment)
+        @polyA = segment
+      end
+
+    end # class Gene
+
+
+    # = Container class of a predicted gene structure.
+    class Exon
+
+      #
+      TYPES = {
+        'Init' => 'Initial exon', 
+        'Intr' => 'Internal exon',
+        'Term' => 'Terminal exon',
+        'Sngl' => 'Single-exon gene',
+        'Prom' => 'Promoter',
+        'PlyA' => 'poly-A signal'
+      }
+
+
+      # Bio::Genescan::Report::Exon.parser
+      def self.parser(line)
+        e = line.strip.split(/ +/)
+        case line
+        when /PlyA/, /Prom/
+          e[12] = e[6].clone
+          e[11] = 0
+          [6,7,8,9,10].each {|i| e[i] = nil }
+        end
+        self.new(e[0], e[1], e[2], e[3], e[4], e[5], e[6], 
+                 e[7], e[8], e[9], e[10], e[11], e[12])
+      end
+
+
+      # Returns
+      attr_reader :gene_number
+
+      # Returns "Ex", exon number field
+      attr_reader :number
+
+      # Returns "Type" field.
+      attr_reader :exon_type
+
+      # Returns "S" field.
+      attr_reader :strand
+
+      # Returns Returns first position of the region. "Begin" field.
+      attr_reader :first
+
+      # Returns Returns last position of the region. "End" field.
+      attr_reader :last
+
+      # Returns "Fr" field.
+      attr_reader :frame
+
+      # Returns "Ph" field.
+      attr_reader :phase
+
+      # Returns "CodRg" field.
+      attr_reader :score
+
+      # Returns "P" field.
+      attr_reader :p_value
+
+      # Returns "Tscr" field.
+      attr_reader :t_score
+      alias_method :coding_region_score, :score 
+
+      
+      # Bio::Genescan::Report::Exon.new(gene_number, exon_type, strand, first, 
+      # end, length, frame, phase, acceptor_score, donor_score, score, p_value, 
+      # t_score)
+      def initialize(gnex, t, s, b, e, len, fr, ph, iac, dot, cr, prob, ts)
+        @gene_number, @number = gnex.split(".").map {|n| n.to_i }
+        @exon_type = t
+        @strand    = s
+        @first     = b.to_i
+        @last      = e.to_i
+        @length    = len.to_i
+        @frame     = fr
+        @phase     = ph
+        @i_ac      = iac.to_i
+        @do_t      = dot.to_i
+        @score     = cr.to_i
+        @p_value   = prob.to_f
+        @t_score   = ts.to_f
+      end
+
+
+
+      # Bio::Genescan::Report::Exon#exon_type_long      
+      #
+      # Returns a human-readable "Type" of exon.
+      def exon_type_long
+        TYPES[exon_type]
+      end
+
+        
+      # Bio::Genescan::Report::Exon#range
+      #
+      # Returns Range object of the region.
+      def range 
+        Range.new(@first, @last)
+      end
+
+
+      # Bio::Genescan::Report::Exon#acceptor_score
+      #
+      # "I/Ac" field.
+      def acceptor_score
+        @i_ac
+      end
+      alias_method :initiation_score, :acceptor_score 
+
+
+      # Bio::Genescan::Report::Exon#donor_score
+      #
+      # "Do/T" field.
+      def donor_score
+        @do_t
+      end
+      alias_method :termination_score, :donor_score 
+
+    end # class Exon
+    
+  end # class Report
+  
+end # class Genscan
+
+end # module Bio
+
+
+
+
+
+# testing code
+
+if __FILE__ == $0
+
+  if $<.filename != '-'
+    report = $<.read
+  else
+    report = File.open(__FILE__,  'r').read.scan(/^>>>> (.+)$/).join("\n")
+  end
+
+
+  puts "= class Bio::Genscan::Report "
+  report = Bio::Genscan::Report.new(report)
+
+
+  print " report.genscan_version #=> "
+  p report.genscan_version
+  print " report.date_run #=> "
+  p report.date_run
+  print " report.time #=> "
+  p report.time
+
+  print " report.query_name #=> "
+  p report.query_name
+  print " report.length #=> "
+  p report.length
+  print " report.gccontent #=> "
+  p report.gccontent
+  print " report.isochore #=> "
+  p report.isochore
+
+  print " report.matrix #=> " 
+  p report.matrix
+
+  puts " report.predictions (Array of Bio::Genscan::Report::Gene)  " 
+  print " report.predictions.size #=> "
+  p report.predictions.size
+
+
+  report.predictions.each {|gene|
+    puts "\n== class Bio::Genscan::Report::Gene "
+    print " gene.number #=> " 
+    p gene.number
+    print " gene.aaseq (Bio::FastaFormat) #=> " 
+    p gene.aaseq
+    print " gene.naseq (Bio::FastaFormat) #=> " 
+    p gene.naseq
+    print " ene.promoter (Bio::Genscan::Report::Exon) #=> " 
+    p gene.promoter
+    print " gene.polyA (Bio::Genscan::Report::Exon) #=> " 
+    p gene.polyA
+    puts " gene.exons (Array of Bio::Genscan::Report::Exon) " 
+    print " gene.exons.size #=> " 
+    p gene.exons.size
+
+
+    gene.exons.each {|exon|
+      puts "\n== class Bio::Genscan::Report::Exon "
+      print " exon.number #=> "
+      p exon.number
+      print " exon.exon_type #=> "
+      p exon.exon_type
+      print " exon.exon_type_long #=> "
+      p exon.exon_type_long
+      print " exon.strand #=> "
+      p exon.strand
+      print " exon.first #=> "
+      p exon.first
+      print " exon.last #=> "
+      p exon.last
+      print " exon.range (Range) #=> "
+      p exon.range
+      print " exon.frame #=> "
+      p exon.frame
+      print " exon.phase #=> "
+      p exon.phase
+      print " exon.acceptor_score #=> "
+      p exon.acceptor_score
+      print " exon.donor_score #=> "
+      p exon.donor_score
+      print " exon.initiation_score #=> "
+      p exon.initiation_score
+      print " exon.termination_score #=> "
+      p exon.termination_score
+      print " exon.score #=> "
+      p exon.score
+      print " exon.p_value #=> "
+      p exon.p_value
+      print " exon.t_score #=> "
+      p exon.t_score
+      puts
+    }
+    puts
+  }
+
+end
+
+
+
+
+
+=begin
+
+
+= Sample Genscan report with '^>>>> '.
+
+
+>>>> GENSCAN 1.0	Date run: 30-May-103	Time: 14:06:28
+>>>> 
+>>>> Sequence HUMRASH : 12942 bp : 68.17% C+G : Isochore 4 (57 - 100 C+G%)
+>>>> 
+>>>> Parameter matrix: HumanIso.smat
+>>>> 
+>>>> Predicted genes/exons:
+>>>> 
+>>>> Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..
+>>>> ----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------
+>>>> 
+>>>>  1.01 Init +   1664   1774  111  1  0   94   83   212 0.997  21.33
+>>>>  1.02 Intr +   2042   2220  179  1  2  104   66   408 0.997  40.12
+>>>>  1.03 Intr +   2374   2533  160  1  1   89   94   302 0.999  32.08
+>>>>  1.04 Term +   3231   3350  120  2  0  115   48   202 0.980  18.31
+>>>>  1.05 PlyA +   3722   3727    6                              -5.80
+>>>> 
+>>>>  2.00 Prom +   6469   6508   40                              -7.92
+>>>>  2.01 Init +   8153   8263  111  1  0   94   83   212 0.998  21.33
+>>>>  2.02 Intr +   8531   8709  179  1  2  104   66   408 0.997  40.12
+>>>>  2.03 Intr +   8863   9022  160  1  1   89   94   302 0.999  32.08
+>>>>  2.04 Term +   9720   9839  120  2  0  115   48   202 0.961  18.31
+>>>> 
+>>>> Predicted peptide sequence(s):
+>>>> 
+>>>> Predicted coding sequence(s):
+>>>> 
+>>>> 
+>>>> >HUMRASH|GENSCAN_predicted_peptide_1|189_aa
+>>>> MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
+>>>> QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
+>>>> AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPG
+>>>> CMSCKCVLS
+>>>> 
+>>>> >HUMRASH|GENSCAN_predicted_CDS_1|570_bp
+>>>> atgacggaatataagctggtggtggtgggcgccggcggtgtgggcaagagtgcgctgacc
+>>>> atccagctgatccagaaccattttgtggacgaatacgaccccactatagaggattcctac
+>>>> cggaagcaggtggtcattgatggggagacgtgcctgttggacatcctggataccgccggc
+>>>> caggaggagtacagcgccatgcgggaccagtacatgcgcaccggggagggcttcctgtgt
+>>>> gtgtttgccatcaacaacaccaagtcttttgaggacatccaccagtacagggagcagatc
+>>>> aaacgggtgaaggactcggatgacgtgcccatggtgctggtggggaacaagtgtgacctg
+>>>> gctgcacgcactgtggaatctcggcaggctcaggacctcgcccgaagctacggcatcccc
+>>>> tacatcgagacctcggccaagacccggcagggagtggaggatgccttctacacgttggtg
+>>>> cgtgagatccggcagcacaagctgcggaagctgaaccctcctgatgagagtggccccggc
+>>>> tgcatgagctgcaagtgtgtgctctcctga
+>>>> 
+>>>> >HUMRASH|GENSCAN_predicted_peptide_2|189_aa
+>>>> MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
+>>>> QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
+>>>> AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPG
+>>>> CMSCKCVLS
+>>>> 
+>>>> >HUMRASH|GENSCAN_predicted_CDS_2|570_bp
+>>>> atgacggaatataagctggtggtggtgggcgccggcggtgtgggcaagagtgcgctgacc
+>>>> atccagctgatccagaaccattttgtggacgaatacgaccccactatagaggattcctac
+>>>> cggaagcaggtggtcattgatggggagacgtgcctgttggacatcctggataccgccggc
+>>>> caggaggagtacagcgccatgcgggaccagtacatgcgcaccggggagggcttcctgtgt
+>>>> gtgtttgccatcaacaacaccaagtcttttgaggacatccaccagtacagggagcagatc
+>>>> aaacgggtgaaggactcggatgacgtgcccatggtgctggtggggaacaagtgtgacctg
+>>>> gctgcacgcactgtggaatctcggcaggctcaggacctcgcccgaagctacggcatcccc
+>>>> tacatcgagacctcggccaagacccggcagggagtggaggatgccttctacacgttggtg
+>>>> cgtgagatccggcagcacaagctgcggaagctgaaccctcctgatgagagtggccccggc
+>>>> tgcatgagctgcaagtgtgtgctctcctga
+
+=end