bio 1.3.1 → 1.4.0

data/lib/bio/db/sanger_chromatogram/chromatogram.rb

@@ -0,0 +1,133 @@
+#
+# = bio/db/sanger_chromatogram/chromatogram.rb - Sanger Chromatogram class 
+#
+# Copyright::	Copyright (C) 2009 Anthony Underwood <anthony.underwood@hpa.org.uk>, <email2ants@gmail.com>
+# License::	The Ruby License
+#
+# $Id:$
+#
+require 'bio/sequence/adapter'
+module Bio
+  # == Description
+  #
+  # This is the Superclass for the Abif and Scf classes that allow importing of the common scf
+  # and abi sequence chromatogram formats
+  # The following attributes are Common to both the Abif and Scf subclasses
+  #
+  # * *chromatogram_type* (String): This is extracted from the chromatogram file itself and will 
+  #   probably be either .scf or ABIF for Scf and Abif files respectively.
+  # * *version* (String): The version of the Scf or Abif file
+  # * *sequence* (String): the sequence contained within the chromatogram as a string.
+  # * *qualities* (Array): the quality scores of each base as an array of integers. These will
+  #   probably be phred scores.
+  # * *peak_indices* (Array): if the sequence traces contained within the chromatogram are imagined   
+  #   as being plotted on an x,y graph, the peak indices are the x positions of the peaks that  
+  #   represent the nucleotides bases found in the sequence from the chromatogram. For example if  
+  #   the peak_indices are [16,24,37,49 ....] and the sequence is AGGT...., at position 16 the  
+  #   traces in the chromatogram were base-called as an A, position 24 a G, position 37 a G,
+  #   position 49 a T etc
+  # * *atrace*, *ctrace*, *gtrace*, *ttrace* (Array): If the sequence traces contained within 
+  #   the chromatogram are imagined as being plotted on an x,y graph, these attributes are arrays of 
+  #   y positions for each of the 4 nucleotide bases along the length of the x axis. If these were 
+  #   plotted joined by lines of different colours then the resulting graph should look like the
+  #   original chromatogram file when viewed in a chromtogram viewer such as Chromas, 4Peaks or
+  #   FinchTV.
+  # * *dye_mobility* (String):  The mobility of the dye used when sequencing. This can influence the 
+  #   base calling
+  #
+  # == Usage
+  #   filename = "path/to/sequence_chromatogram_file"
+  # 
+  # for Abif files
+  #   chromatogram_ff = Bio::Abif.open(filename)
+  # for Scf files
+  #   chromatogram_ff = Bio::Scf.open(filename)
+  #
+  #   chromatogram = chromatogram_ff.next_entry
+  #   chromatogram.to_seq # => returns a Bio::Sequence object
+  #   chromatogram.sequence # => returns the sequence contained within the chromatogram as a string
+  #   chromatogram.qualities # => returns an array of quality values for each base
+  #   chromatogram.atrace # => returns an array of the a trace y positions
+  #
+  class SangerChromatogram
+    # The type of chromatogram file .scf for Scf files and ABIF doe Abif files
+    attr_accessor :chromatogram_type
+    # The Version of the Scf or Abif file (String)
+    attr_accessor :version
+    # The sequence contained within the chromatogram (String)
+    attr_accessor :sequence
+    # An array of quality scores for each base in the sequence (Array) 
+    attr_accessor :qualities
+    # An array  'x' positions (see description) on the trace where the bases occur/have been called (Array)
+    attr_accessor :peak_indices
+    # An array of 'y' positions (see description) for the 'A' trace from the chromatogram (Array
+    attr_accessor :atrace
+    # An array of 'y' positions (see description) for the 'C' trace from the chromatogram (Array
+    attr_accessor :ctrace
+    # An array of 'y' positions (see description) for the 'G' trace from the chromatogram (Array
+    attr_accessor :gtrace
+    # An array of 'y' positions (see description) for the 'T' trace from the chromatogram (Array
+    attr_accessor :ttrace
+    #The mobility of the dye used when sequencing (String)
+    attr_accessor :dye_mobility
+
+    def self.open(filename)
+      Bio::FlatFile.open(self, filename)
+    end
+    
+    # Returns a Bio::Sequence::NA object based on the sequence from the chromatogram
+    def seq
+      Bio::Sequence::NA.new(@sequence)
+    end
+    
+    # Returns a Bio::Sequence object based on the sequence from the chromatogram
+    def to_biosequence
+      Bio::Sequence.adapter(self, Bio::Sequence::Adapter::SangerChromatogram)
+    end
+    alias :to_seq :to_biosequence
+    
+    # Returns the sequence from the chromatogram as a string
+    def sequence_string
+      @sequence
+    end
+    
+    # Reverses and complements the current chromatogram object including its sequence, traces
+    # and qualities
+    def complement!
+      # reverse traces
+      tmp_trace = @atrace
+      @atrace = @ttrace.reverse
+      @ttrace = tmp_trace.reverse
+      tmp_trace = @ctrace
+      @ctrace = @gtrace.reverse
+      @gtrace = tmp_trace.reverse
+
+      # reverse base qualities
+      if !@aqual.nil? # if qualities exist
+        tmp_qual = @aqual
+        @aqual = @tqual.reverse
+        @tqual = tmp_qual.reverse
+        tmp_qual = @cqual
+        @cqual = @gqual.reverse
+        @gqual = tmp_qual.reverse
+      end
+
+      #reverse qualities
+      @qualities = @qualities.reverse
+
+      #reverse peak indices
+      @peak_indices = @peak_indices.map{|index| @atrace.size - index}
+      @peak_indices.reverse!
+
+      # reverse sequence
+      @sequence = @sequence.reverse.tr('atgcnrykmswbvdh','tacgnyrmkswvbhd')
+    end
+    # Returns a new chromatogram object of the appropriate subclass (scf or abi) where the 
+    # sequence, traces and qualities have all been revesed and complemented
+    def complement
+      chromatogram = self.dup
+      chromatogram.complement!
+      return chromatogram
+    end
+  end
+end

data/lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb

@@ -0,0 +1,32 @@
+#
+# = bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb - Bio::SangerChromatogram to Bio::Sequence adapter module
+#
+# Copyright::	Copyright (C) 2009 Anthony Underwood <anthony.underwood@hpa.org.uk>, <email2ants@gmail.com>
+# License::	The Ruby License
+#
+# $Id:$
+#
+
+require 'bio/sequence'
+require 'bio/sequence/adapter'
+
+# Internal use only. Normal users should not use this module.
+#
+# Bio::SangerChromatogram to Bio::Sequence adapter module.
+# It is internally used in Bio::SangerChromatogram#to_biosequence.
+#
+module Bio::Sequence::Adapter::SangerChromatogram
+
+  extend Bio::Sequence::Adapter
+
+  private
+
+  def_biosequence_adapter :seq
+
+  # primary accession
+  def_biosequence_adapter :primary_accession do |orig|
+    orig.version
+  end
+
+end #module Bio::Sequence::Adapter::SangerChromatogram
+

data/lib/bio/db/sanger_chromatogram/scf.rb

@@ -0,0 +1,210 @@
+#
+# = bio/db/sanger_chromatogram/scf.rb - Scf class 
+#
+# Copyright::	Copyright (C) 2009 Anthony Underwood <anthony.underwood@hpa.org.uk>, <email2ants@gmail.com>
+# License::	The Ruby License
+#
+
+require 'bio/db/sanger_chromatogram/chromatogram'
+
+module Bio
+  # == Description
+  #
+  # This class inherits from the SangerChromatogram superclass. It captures the information contained
+  # within an scf format chromatogram file generated by DNA sequencing. See the SangerChromatogram class
+  # for usage
+  class Scf < SangerChromatogram
+    # sequence attributes
+    
+    # The quality of each base at each position along the length of the sequence is captured
+    # by the nqual attributes where n is one of a, c, g or t. Generally the quality will be
+    # high for the base that is called at a particular position and low for all the other bases.
+    # However at positions of poor sequence quality, more than one base may have similar top scores.
+    # By analysing the nqual attributes it may be possible to determine if the base calling was
+    # correct or not.
+    # The quality of the A base at each sequence position
+    attr_accessor :aqual
+    # The quality of the C base at each sequence position
+    attr_accessor :cqual
+    # The quality of the G base at each sequence position
+    attr_accessor :gqual
+    # The quality of the T base at each sequence position
+    attr_accessor :tqual
+    # A hash of extra information extracted from the chromatogram file
+    attr_accessor :comments
+    
+    # see SangerChromatogram class for how to create an Scf object and its usage
+    def initialize(string)
+      header = string.slice(0,128)
+      # read in header info
+      @chromatogram_type, @samples, @sample_offset, @bases, @bases_left_clip, @bases_right_clip, @bases_offset, @comment_size, @comments_offset, @version, @sample_size, @code_set, @header_spare = header.unpack("a4 NNNNNNNN a4 NN N20")
+      get_traces(string)
+      get_bases_peakIndices_and_qualities(string)
+      get_comments(string)
+      if @comments["DYEP"]
+        @dye_mobility = @comments["DYEP"]
+      else
+        @dye_mobility = "Unnown"
+      end
+    end
+
+    private
+
+    def get_traces(string)
+      if @version == "3.00"
+        # read in trace info
+        offset = @sample_offset
+        length = @samples * @sample_size
+        # determine whether the data is stored in 1 byte as an unsigned byte or 2 bytes as an  unsigned short
+        @sample_size == 2 ? byte = "n" : byte = "c"
+        for base in ["a" , "c" , "g" , "t"]
+          trace_read = string.slice(offset,length).unpack("#{byte}#{@samples}")
+          # convert offsets
+          for sample_num in (0..trace_read.size-1)
+            if trace_read[sample_num] > 30000
+              trace_read[sample_num] = trace_read[sample_num] - 65536
+            end
+          end
+          # For 8-bit data we need to emulate a signed/unsigned
+          # cast that is implicit in the C implementations.....
+          if @sample_size == 1
+            for sample_num in (0..trace_read.size-1)
+              trace_read[sample_num] += 256 if trace_read[sample_num] < 0
+            end
+          end
+          trace_read = convert_deltas_to_values(trace_read)
+          self.instance_variable_set("@#{base}trace", trace_read)
+          offset += length
+        end
+      elsif @version == "2.00"
+        @atrace = []
+        @ctrace = []
+        @gtrace = []
+        @ttrace = []
+        # read in trace info
+        offset = @sample_offset
+        length = @samples * @sample_size * 4
+        # determine whether the data is stored in 1 byte as an unsigned byte or 2 bytes as an  unsigned short
+        @sample_size == 2 ? byte = "n" : byte = "c"
+        trace_read = string.slice(offset,length).unpack("#{byte}#{@samples*4}")
+        (0..(@samples-1)*4).step(4) do |offset2|
+          @atrace << trace_read[offset2]
+          @ctrace << trace_read[offset2+1]
+          @gtrace << trace_read[offset2+2]
+          @ttrace << trace_read[offset2+3]
+        end
+      end
+    end
+    def get_bases_peakIndices_and_qualities(string)
+      if @version == "3.00"
+        # now go and get the peak index information
+        offset = @bases_offset
+        length = @bases * 4
+        get_v3_peak_indices(string,offset,length)
+
+        # now go and get the accuracy information
+        offset += length;
+        get_v3_accuracies(string,offset,length)
+
+        # OK, now go and get the base information.
+        offset += length;
+        length = @bases;
+        get_v3_sequence(string,offset,length)
+
+        #combine accuracies to get quality scores
+        @qualities= convert_accuracies_to_qualities
+      elsif @version == "2.00"
+        @peak_indices = []
+        @aqual = []
+        @cqual = []
+        @gqual = []
+        @tqual = []
+        @qualities = []
+        @sequence = ""
+        # now go and get the base information
+        offset = @bases_offset
+        length = @bases * 12
+        all_bases_info = string.slice(offset,length)
+
+        (0..length-1).step(12) do |offset2|
+          base_info = all_bases_info.slice(offset2,12).unpack("N C C C C a C3")
+          @peak_indices << base_info[0]
+          @aqual << base_info[1]
+          @cqual << base_info[2]
+          @gqual << base_info[3]
+          @tqual << base_info[4]
+          @sequence += base_info[5].downcase
+          case base_info[5].downcase
+          when "a"
+            @qualities << base_info[1]
+          when "c"
+            @qualities << base_info[2]
+          when "g"
+            @qualities << base_info[3]
+          when "t"
+            @qualities << base_info[4]
+          else
+            @qualities << 0
+          end
+        end
+      end
+    end
+    def get_v3_peak_indices(string,offset,length)
+      @peak_indices = string.slice(offset,length).unpack("N#{length/4}")
+    end
+    def get_v3_accuracies(string,offset,length)
+      qualities   = string.slice(offset,length)
+      qual_length = length/4;
+      qual_offset = 0;
+      for base in ["a" , "c" , "g" , "t"]
+        self.instance_variable_set("@#{base}qual",qualities.slice(qual_offset,qual_length).unpack("C#{qual_length}"))
+        qual_offset += qual_length
+      end
+    end
+    def get_v3_sequence(string,offset,length)
+      @sequence = string.slice(offset,length).unpack("a#{length}").join('').downcase
+    end
+
+    def convert_deltas_to_values(trace_read)
+      p_sample = 0;
+      for sample_num in (0..trace_read.size-1)
+        trace_read[sample_num] = trace_read[sample_num] + p_sample
+        p_sample = trace_read[sample_num];
+      end
+      p_sample = 0;
+      for sample_num in (0..trace_read.size-1)
+        trace_read[sample_num] = trace_read[sample_num] + p_sample
+        p_sample = trace_read[sample_num];
+      end
+      return trace_read
+    end
+    def convert_accuracies_to_qualities
+      qualities = Array.new
+      for base_pos in (0..@sequence.length-1)
+        case sequence.slice(base_pos,1)
+        when "a"
+          qualities << @aqual[base_pos]
+        when "c"
+          qualities << @cqual[base_pos]
+        when "g"
+          qualities << @gqual[base_pos]
+        when "t"
+          qualities << @tqual[base_pos]
+        else
+          qualities << 0
+        end
+      end
+      return qualities
+    end
+    def get_comments(string)
+      @comments = Hash.new
+      comment_string = string.slice(@comments_offset,@comment_size)
+      comment_string.gsub!(/\0/, "")
+      comment_array = comment_string.split("\n")
+      comment_array.each do |comment|
+        comment =~ /(\w+)=(.*)/
+        @comments[$1] = $2
+      end
+    end
+  end
+end

data/lib/bio/io/das.rb

@@ -415,47 +415,3 @@ end
 
 end # module Bio
 
-
-if __FILE__ == $0
-
-# begin
-#   require 'pp'
-#   alias p pp
-# rescue LoadError
-# end
-
-  puts "### WormBase"
-  wormbase = Bio::DAS.new('http://www.wormbase.org/db/')
-
-  puts ">>> test get_dsn"
-  p wormbase.get_dsn
-
-  puts ">>> create segment obj Bio::DAS::SEGMENT.region('I', 1, 1000)"
-  seg = Bio::DAS::SEGMENT.region('I', 1, 1000)
-  p seg
-
-  puts ">>> test get_dna"
-  p wormbase.get_dna('elegans', seg)
-
-  puts "### test get_features"
-  p wormbase.get_features('elegans', seg)
-
-  puts "### KEGG DAS"
-  kegg_das = Bio::DAS.new("http://das.hgc.jp/cgi-bin/")
-
-  dsn_list = kegg_das.get_dsn
-  org_list = dsn_list.collect {|x| x.source}
-
-  puts ">>> dsn : entry_points"
-  org_list.each do |org|
-    print "#{org} : "
-    list = kegg_das.get_entry_points(org)
-    list.segments.each do |seg|
-      print " #{seg.entry_id}"
-    end
-    puts
-  end
-
-end
-
-

data/lib/bio/io/ddbjxml.rb

@@ -5,7 +5,7 @@
 #		Toshiaki Katayama <k@bioruby.org>
 # License::	The Ruby License
 #
-# $Id: ddbjxml.rb,v 1.14 2007/04/05 23:35:41 trevor Exp $
+# $Id:$
 #
 
 require 'bio/io/soapwsdl'
@@ -456,183 +456,3 @@ end # XML
 end # DDBJ
 end # Bio
 
-
-
-if __FILE__ == $0
-
-  begin
-    require 'pp'
-    alias p pp
-  rescue LoadError
-  end
-
-  puts ">>> Bio::DDBJ::XML::Blast"
-  serv = Bio::DDBJ::XML::Blast.new
-# serv.log = STDERR
-
-  query = "MSSRIARALALVVTLLHLTRLALSTCPAACHCPLEAPKCAPGVGLVRDGCGCCKVCAKQL"
-
-  puts "### searchSimple('blastp', 'SWISS', query)"
-  puts serv.searchSimple('blastp', 'SWISS', query)
-
-  puts "### searchParam('tblastn', 'ddbjvrl', query, '-m 8')"
-  puts serv.searchParam('tblastn', 'ddbjvrl', query, '-m 8')
-
-
-  puts ">>> Bio::DDBJ::XML::ClustalW"
-  serv = Bio::DDBJ::XML::ClustalW.new
-
-  query = <<END
-> RABSTOUT   rabbit Guinness receptor
-   LKMHLMGHLKMGLKMGLKGMHLMHLKHMHLMTYTYTTYRRWPLWMWLPDFGHAS
-   ADSCVCAHGFAVCACFAHFDVCFGAVCFHAVCFAHVCFAAAVCFAVCAC
-> MUSNOSE   mouse nose drying factor
-    mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt
-    fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv
-> HSHEAVEN    human Guinness receptor repeat
- mhkmmhkgmkhmhgmhmhg   lhmkmhlkmgkhmgkmk  ytytytryrwtqtqwtwyt
- fdgfdsgafdagfdgfsag   dfavdfdvgavfsvfgv  dfsvdgvagvfdv
- mhkmmhkgmkhmhgmhmhg   lhmkmhlkmgkhmgkmk  ytytytryrwtqtqwtwyt
- fdgfdsgafdagfdgfsag   dfavdfdvgavfsvfgv  dfsvdgvagvfdv
-END
-
-  puts "### analyzeSimple(query)"
-  puts serv.analyzeSimple(query)
-
-  puts "### analyzeParam(query, '-align -matrix=blosum')"
-  puts serv.analyzeParam(query, '-align -matrix=blosum')
-
-
-  puts ">>> Bio::DDBJ::XML::DDBJ"
-  serv = Bio::DDBJ::XML::DDBJ.new
-
-  puts "### getFFEntry('AB000050')"
-  puts serv.getFFEntry('AB000050')
-
-  puts "### getXMLEntry('AB000050')"
-  puts serv.getXMLEntry('AB000050')
-
-  puts "### getFeatureInfo('AB000050', 'cds')"
-  puts serv.getFeatureInfo('AB000050', 'cds')
-
-  puts "### getAllFeatures('AB000050')"
-  puts serv.getAllFeatures('AB000050')
-
-  puts "### getRelatedFeatures('AL121903', '59000', '64000')"
-  puts serv.getRelatedFeatures('AL121903', '59000', '64000')
-
-  puts "### getRelatedFeaturesSeq('AL121903', '59000', '64000')"
-  puts serv.getRelatedFeaturesSeq('AL121903', '59000', '64000')
-
-
-  puts ">>> Bio::DDBJ::XML::Fasta"
-  serv = Bio::DDBJ::XML::Fasta.new
-
-  query = ">Test\nMSDGAVQPDG GQPAVRNERA TGSGNGSGGG GGGGSGGVGI"
-
-  puts "### searchSimple('fasta34', 'PDB', query)"
-  puts serv.searchSimple('fasta34', 'PDB', query)
-
-  query = ">Test\nAGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"
-
-  puts "### searchParam('fastx34_t', 'PDB', query, '-n')"
-  puts serv.searchParam('fastx34_t', 'PDB', query, '-n')
-
-
-  puts ">>> Bio::DDBJ::XML::GetEntry"
-  serv = Bio::DDBJ::XML::GetEntry.new
-
-  puts "### getDDBJEntry('AB000050')"
-  puts serv.getDDBJEntry('AB000050')
-
-  puts "### getPDBEntry('1AAR')"
-  puts serv. getPDBEntry('1AAR')
-
-
-  puts ">>> Bio::DDBJ::XML::Gib"
-  serv = Bio::DDBJ::XML::Gib.new
-
-  puts "### getOrganismList"
-  puts serv.getOrganismList
-
-  puts "### getChIDList"
-  puts serv.getChIDList
-
-  puts "### getOrganismNameFromChid('Sent_CT18:')"
-  puts serv.getOrganismNameFromChid('Sent_CT18:')
-
-  puts "### getChIDFromOrganismName('Aquifex aeolicus VF5')"
-  puts serv.getChIDFromOrganismName('Aquifex aeolicus VF5')
-
-  puts "### getAccession('Ecol_K12_MG1655:')"
-  puts serv.getAccession('Ecol_K12_MG1655:')
-
-  puts "### getPieceNumber('Mgen_G37:')"
-  puts serv.getPieceNumber('Mgen_G37:')
-
-  puts "### getDivision('Mgen_G37:')"
-  puts serv.getDivision('Mgen_G37:')
-
-  puts "### getType('Mgen_G37:')"
-  puts serv.getType('Mgen_G37:')
-
-  puts "### getCDS('Aaeo_VF5:ece1')"
-  puts serv.getCDS('Aaeo_VF5:ece1')
-
-  puts "### getFlatFile('Nost_PCC7120:pCC7120zeta')"
-  puts serv.getFlatFile('Nost_PCC7120:pCC7120zeta')
-
-  puts "### getFastaFile('Nost_PCC7120:pCC7120zeta')"
-  puts serv.getFastaFile('Nost_PCC7120:pCC7120zeta', 'cdsaa')
-
-
-  puts ">>> Bio::DDBJ::XML::Gtop"
-  serv = Bio::DDBJ::XML::Gtop.new
-
-  puts "### getOrganismList"
-  puts serv.getOrganismList
-
-  puts "### getMasterInfo"
-  puts serv.getMasterInfo('thrA', 'ecol0')
-
-
-#  puts ">>> Bio::DDBJ::XML::PML"
-#  serv = Bio::DDBJ::XML::PML.new
-#
-#  puts "### getVariation('1')"
-#  puts serv.getVariation('1')
-
-
-  puts ">>> Bio::DDBJ::XML::SRS"
-  serv = Bio::DDBJ::XML::SRS.new
-
-  puts "### searchSimple('[pathway-des:sugar]')"
-  puts serv.searchSimple('[pathway-des:sugar]')
-
-  puts "### searchParam('[swissprot-des:cohesin]', '-f seq -sf fasta')"
-  puts serv.searchParam('[swissprot-des:cohesin]', '-f seq -sf fasta')
-
-
-  puts ">>> Bio::DDBJ::XML::TxSearch"
-  serv = Bio::DDBJ::XML::TxSearch.new
-
-  puts "### searchSimple('*coli')"
-  puts serv.searchSimple('*coli')
-
-  puts "### searchSimple('*tardigrada*')"
-  puts serv.searchSimple('*tardigrada*')
-
-  puts "### getTxId('Escherichia coli')"
-  puts serv.getTxId('Escherichia coli')
-
-  puts "### getTxName('562')"
-  puts serv.getTxName('562')
-
-  query = "Campylobacter coli\nEscherichia coli"
-  rank = "family\ngenus"
-
-  puts "### searchLineage(query, rank, 'Bacteria')"
-  puts serv.searchLineage(query, rank, 'Bacteria')
-
-end
-