bio 1.3.1 → 1.4.0

data/lib/bio/data/codontable.rb

@@ -5,7 +5,7 @@
 #		Toshiaki Katayama <k@bioruby.org>
 # License::	The Ruby License
 #
-# $Id: codontable.rb,v 0.18 2007/04/05 23:35:40 trevor Exp $
+# $Id:$
 #
 # == Data source
 #
@@ -626,97 +626,3 @@ end # CodonTable
 
 end # module Bio
 
-
-if __FILE__ == $0
-
-  begin
-    require 'pp'
-    alias p pp
-  rescue LoadError
-  end
-
-  puts "### Bio::CodonTable[1]"
-  p ct1 = Bio::CodonTable[1]
-
-  puts ">>> Bio::CodonTable#table"
-  p ct1.table
-
-  puts ">>> Bio::CodonTable#each"
-  ct1.each do |codon, aa|
-    puts "#{codon} -- #{aa}"
-  end
-
-  puts ">>> Bio::CodonTable#definition"
-  p ct1.definition
-
-  puts ">>> Bio::CodonTable#['atg']"
-  p ct1['atg']
-
-  puts ">>> Bio::CodonTable#revtrans('A')"
-  p ct1.revtrans('A')
-
-  puts ">>> Bio::CodonTable#start_codon?('atg')"
-  p ct1.start_codon?('atg')
-  
-  puts ">>> Bio::CodonTable#start_codon?('aaa')"
-  p ct1.start_codon?('aaa')
-
-  puts ">>> Bio::CodonTable#stop_codon?('tag')"
-  p ct1.stop_codon?('tag')
-  
-  puts ">>> Bio::CodonTable#stop_codon?('aaa')"
-  p ct1.stop_codon?('aaa')
-
-  puts ">>> ct1_copy = Bio::CodonTable.copy(1)"
-  p ct1_copy = Bio::CodonTable.copy(1)
-  puts ">>> ct1_copy['tga'] = 'U'"
-  p ct1_copy['tga'] = 'U'
-  puts " orig : #{ct1['tga']}"
-  puts " copy : #{ct1_copy['tga']}"
-
-
-  puts "### ct = Bio::CodonTable.new(hash, definition)"
-  hash = {
-    'ttt' => 'F', 'tct' => 'S', 'tat' => 'Y', 'tgt' => 'C',
-    'ttc' => 'F', 'tcc' => 'S', 'tac' => 'Y', 'tgc' => 'C',
-    'tta' => 'L', 'tca' => 'S', 'taa' => '*', 'tga' => 'U',
-    'ttg' => 'L', 'tcg' => 'S', 'tag' => '*', 'tgg' => 'W',
-
-    'ctt' => 'L', 'cct' => 'P', 'cat' => 'H', 'cgt' => 'R',
-    'ctc' => 'L', 'ccc' => 'P', 'cac' => 'H', 'cgc' => 'R',
-    'cta' => 'L', 'cca' => 'P', 'caa' => 'Q', 'cga' => 'R',
-    'ctg' => 'L', 'ccg' => 'P', 'cag' => 'Q', 'cgg' => 'R',
-
-    'att' => 'I', 'act' => 'T', 'aat' => 'N', 'agt' => 'S',
-    'atc' => 'I', 'acc' => 'T', 'aac' => 'N', 'agc' => 'S',
-    'ata' => 'I', 'aca' => 'T', 'aaa' => 'K', 'aga' => 'R',
-    'atg' => 'M', 'acg' => 'T', 'aag' => 'K', 'agg' => 'R',
-
-    'gtt' => 'V', 'gct' => 'A', 'gat' => 'D', 'ggt' => 'G',
-    'gtc' => 'V', 'gcc' => 'A', 'gac' => 'D', 'ggc' => 'G',
-    'gta' => 'V', 'gca' => 'A', 'gaa' => 'E', 'gga' => 'G',
-    'gtg' => 'V', 'gcg' => 'A', 'gag' => 'E', 'ggg' => 'G',
-  }
-  my_ct = Bio::CodonTable.new(hash, "my codon table")
-
-  puts ">>> ct.definition"
-  puts my_ct.definition
-
-  puts ">>> ct.definition=(str)"
-  my_ct.definition = "selenoproteins (Eukaryote)"
-  puts my_ct.definition
-
-  puts ">>> ct['tga']"
-  puts my_ct['tga']
-
-  puts ">>> ct.revtrans('U')"
-  puts my_ct.revtrans('U')
-
-  puts ">>> ct.stop_codon?('tga')"
-  puts my_ct.stop_codon?('tga')
-
-  puts ">>> ct.stop_codon?('tag')"
-  puts my_ct.stop_codon?('tag')
-
-end
-

data/lib/bio/data/na.rb

@@ -5,7 +5,7 @@
 #		Toshiaki Katayama <k@bioruby.org>
 # License::	The Ruby License
 #
-# $Id: na.rb,v 0.23 2007/04/06 04:41:28 k Exp $
+# $Id:$
 #
 # == Synopsis
 #
@@ -196,28 +196,3 @@ end
 
 end # module Bio
 
-
-if __FILE__ == $0
-
-  puts "### na = Bio::NucleicAcid.new"
-  na = Bio::NucleicAcid.new
-
-  puts "# na.to_re('yrwskmbdhvnatgc')"
-  p na.to_re('yrwskmbdhvnatgc')
-
-  puts "# Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')"
-  p Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')
-
-  puts "# na.weight('A')"
-  p na.weight('A')
-
-  puts "# Bio::NucleicAcid.weight('A')"
-  p Bio::NucleicAcid.weight('A')
-
-  puts "# na.weight('atgc')"
-  p na.weight('atgc')
-
-  puts "# Bio::NucleicAcid.weight('atgc')"
-  p Bio::NucleicAcid.weight('atgc')
-
-end

data/lib/bio/db/aaindex.rb

@@ -7,7 +7,7 @@
 #              Mitsuteru C. Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-# $Id: aaindex.rb,v 1.20 2007/04/05 23:35:40 trevor Exp $
+# $Id:$
 #
 # == Description
 #
@@ -318,40 +318,3 @@ module Bio
 
 end # module Bio
 
-
-if __FILE__ == $0
-  require 'bio/io/fetch'
-
-  puts "### AAindex1 (PRAM900102)"
-  aax1 = Bio::AAindex1.new(Bio::Fetch.query('aaindex', 'PRAM900102', 'raw'))
-  p aax1.entry_id
-  p aax1.definition
-  p aax1.dblinks
-  p aax1.author
-  p aax1.title
-  p aax1.journal
-  p aax1.comment
-  p aax1.correlation_coefficient
-  p aax1.index
-  p aax1
-  puts "### AAindex2 (DAYM780301)"
-  aax2 = Bio::AAindex2.new(Bio::Fetch.query('aaindex', 'DAYM780301', 'raw'))
-  p aax2.entry_id
-  p aax2.definition
-  p aax2.dblinks
-  p aax2.author
-  p aax2.title
-  p aax2.journal
-  p aax1.comment
-  p aax2.rows
-  p aax2.cols
-  p aax2.matrix
-  p aax2.matrix[2,2]
-  p aax2.matrix[2,3]
-  p aax2.matrix[4,3]
-  p aax2.matrix.determinant
-  p aax2.matrix.rank
-  p aax2.matrix.transpose
-  p aax2
-end
-

data/lib/bio/db/fasta.rb

@@ -6,7 +6,7 @@
 #              Toshiaki Katayama <k@bioruby.org>
 # License::    The Ruby License
 #
-# $Id: fasta.rb,v 1.28.2.3 2008/06/20 13:43:36 ngoto Exp $
+# $Id:$
 # 
 # == Description
 # 
@@ -273,138 +273,5 @@ module Bio
 
   end #class FastaFormat
 
-  # Treats a FASTA formatted numerical entry, such as:
-  # 
-  #   >id and/or some comments                    <== comment line
-  #   24 15 23 29 20 13 20 21 21 23 22 25 13      <== numerical data
-  #   22 17 15 25 27 32 26 32 29 29 25
-  # 
-  # The precedent '>' can be omitted and the trailing '>' will be removed
-  # automatically.
-  #
-  # --- Bio::FastaNumericFormat.new(entry)
-  # 
-  # Stores the comment and the list of the numerical data.
-  # 
-  # --- Bio::FastaNumericFormat#definition
-  #
-  # The comment line of the FASTA formatted data.
-  #
-  # * FASTA format (Wikipedia)
-  #   http://en.wikipedia.org/wiki/FASTA_format
-  class FastaNumericFormat < FastaFormat
-
-    # Returns the list of the numerical data (typically the quality score
-    # of its corresponding sequence) as an Array.
-    def data
-      unless @list
-        @list = @data.strip.split(/\s+/).map {|x| x.to_i}
-      end
-      @list
-    end
-
-    # Returns the number of elements in the numerical data.
-    def length
-      data.length
-    end
-
-    # Yields on each elements of the numerical data.
-    def each
-      data.each do |x|
-        yield x
-      end
-    end
-
-    # Returns the n-th element.
-    def [](n)
-      data[n]
-    end
-
-    undef query, blast, fasta, seq, naseq, nalen, aaseq, aalen
-
-  end #class FastaNumericFormat
-
 end #module Bio
 
-if __FILE__ == $0
-
-  f_str = <<END
->sce:YBR160W  CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
-MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG
-VPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME
-GIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL
-KLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC
-IFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP
-QWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES
->sce:YBR274W  CHK1; probable serine/threonine-protein kinase [EC:2.7.1.-] [SP:KB9S_YEAST]
-MSLSQVSPLPHIKDVVLGDTVGQGAFACVKNAHLQMDPSIILAVKFIHVP
-TCKKMGLSDKDITKEVVLQSKCSKHPNVLRLIDCNVSKEYMWIILEMADG
-GDLFDKIEPDVGVDSDVAQFYFQQLVSAINYLHVECGVAHRDIKPENILL
-DKNGNLKLADFGLASQFRRKDGTLRVSMDQRGSPPYMAPEVLYSEEGYYA
-DRTDIWSIGILLFVLLTGQTPWELPSLENEDFVFFIENDGNLNWGPWSKI
-EFTHLNLLRKILQPDPNKRVTLKALKLHPWVLRRASFSGDDGLCNDPELL
-AKKLFSHLKVSLSNENYLKFTQDTNSNNRYISTQPIGNELAELEHDSMHF
-QTVSNTQRAFTSYDSNTNYNSGTGMTQEAKWTQFISYDIAALQFHSDEND
-CNELVKRHLQFNPNKLTKFYTLQPMDVLLPILEKALNLSQIRVKPDLFAN
-FERLCELLGYDNVFPLIINIKTKSNGGYQLCGSISIIKIEEELKSVGFER
-KTGDPLEWRRLFKKISTICRDIILIPN
-END
-
-  f = Bio::FastaFormat.new(f_str)
-  puts "### FastaFormat"
-  puts "# entry"
-  puts f.entry
-  puts "# entry_id"
-  p f.entry_id
-  puts "# definition"
-  p f.definition
-  puts "# data"
-  p f.data
-  puts "# seq"
-  p f.seq
-  puts "# seq.type"
-  p f.seq.type
-  puts "# length"
-  p f.length
-  puts "# aaseq"
-  p f.aaseq
-  puts "# aaseq.type"
-  p f.aaseq.type
-  puts "# aaseq.composition"
-  p f.aaseq.composition
-  puts "# aalen"
-  p f.aalen
-
-  puts
-
-  n_str = <<END
->CRA3575282.F 
-24 15 23 29 20 13 20 21 21 23 22 25 13 22 17 15 25 27 32 26  
-32 29 29 25
-END
-
-  n = Bio::FastaNumericFormat.new(n_str)
-  puts "### FastaNumericFormat"
-  puts "# entry"
-  puts n.entry
-  puts "# entry_id"
-  p n.entry_id
-  puts "# definition"
-  p n.definition
-  puts "# data"
-  p n.data
-  puts "# length"
-  p n.length
-  puts "# percent to ratio by yield"
-  n.each do |x|
-    p x/100.0
-  end
-  puts "# first three"
-  p n[0]
-  p n[1]
-  p n[2]
-  puts "# last one"
-  p n[-1]
-
-end
-

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

@@ -0,0 +1,204 @@
+#
+# = bio/db/fasta/format_qual.rb - Qual format and FastaNumericFormat generater
+#
+# Copyright::   Copyright (C) 2009
+#               Naohisa Goto <ng@bioruby.org>
+# License::    The Ruby License
+#
+# $Id:$
+#
+
+require 'bio/sequence/format'
+require 'bio/sequence/quality_score'
+
+module Bio::Sequence::Format::Formatter
+
+  # INTERNAL USE ONLY, YOU SHOULD NOT USE THIS CLASS.
+  # Simple FastaNumeric format output class for Bio::Sequence.
+  class Fasta_numeric < Bio::Sequence::Format::FormatterBase
+
+    # INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD.
+    #
+    # Creates a new FastaNumericFormat generater object from the sequence.
+    #
+    # It does not care whether the content of the quality score is
+    # consistent with the sequence or not, e.g. it does not check
+    # length of the quality score.
+    #
+    # ---
+    # *Arguments*:
+    # * _sequence_: Bio::Sequence object
+    # * (optional) :header => _header_: (String) (default nil)
+    # * (optional) :width => _width_: (Fixnum) (default 70)
+    def initialize; end if false # dummy for RDoc
+
+    # INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD.
+    #
+    # Output the FASTA format string of the sequence.  
+    #
+    # Currently, this method is used in Bio::Sequence#output like so,
+    #
+    #   s = Bio::Sequence.new('atgc')
+    #   s.quality_scores = [ 70, 80, 90, 100 ]
+    #   puts s.output(:fasta_numeric)
+    # ---
+    # *Returns*:: String object
+    def output
+      header = @options[:header]
+      width = @options.has_key?(:width) ? @options[:width] : 70
+      seq = @sequence.seq.to_s
+      entry_id = @sequence.entry_id || 
+        "#{@sequence.primary_accession}.#{@sequence.sequence_version}"
+      definition = @sequence.definition
+      header ||= "#{entry_id} #{definition}"
+
+      sc = fastanumeric_quality_scores(seq)
+      if width then
+        if width <= 0 then
+          main = sc.join("\n")
+        else
+          len = 0
+          main = sc.collect do |x|
+            str = (len == 0) ? "#{x}" : " #{x}"
+            len += str.size
+            if len > width then
+              len = "#{x}".size
+              str = "\n#{x}"
+            end
+            str
+          end.join('')
+        end
+      else
+        main = sc.join(' ')
+      end
+
+      ">#{header}\n#{main}\n"
+    end
+
+    private
+
+    def fastanumeric_quality_scores(seq)
+      @sequence.quality_scores || []
+    end
+
+  end #class Fasta_numeric
+
+  # INTERNAL USE ONLY, YOU SHOULD NOT USE THIS CLASS.
+  # Simple Qual format (sequence quality) output class for Bio::Sequence.
+  class Qual < Fasta_numeric
+
+    # INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD.
+    #
+    # Creates a new Qual format generater object from the sequence.
+    #
+    # The only difference from Fastanumeric is that Qual outputs
+    # Phred score by default, and data conversion will be performed
+    # if needed. Output score type can be changed by the
+    # ":quality_score_type" option.
+    #
+    # If the sequence have no quality score type information
+    # and no error probabilities, but the score exists,
+    # the score is regarded as :phred (Phred score).
+    #
+    # ---
+    # *Arguments*:
+    # * _sequence_: Bio::Sequence object
+    # * (optional) :header => _header_: (String) (default nil)
+    # * (optional) :width => _width_: (Fixnum) (default 70)
+    # * (optional) :quality_score_type => _type_: (Symbol) (default nil)
+    # * (optional) :default_score => _score_: (Integer) default score for bases that have no valid quality scores or error probabilities (default 0)
+    def initialize; end if false # dummy for RDoc
+
+    private
+
+    def fastanumeric_quality_scores(seq)
+      qsc = qual_quality_scores(seq)
+      if qsc.size > seq.length then
+        qsc = qsc[0, seq.length]
+      elsif qsc.size < seq.length then
+        padding = @options[:default_score] || 0
+        psize = seq.length - qsc.size
+        qsc += Array.new(psize, padding)
+      end
+      qsc
+    end
+
+    def qual_quality_scores(seq)
+      return [] if seq.length <= 0
+
+      # get output quality score type
+      fmt = @options[:quality_score_type]
+
+      qsc = @sequence.quality_scores
+      qsc_type = @sequence.quality_score_type
+
+      # checks if no need to convert
+      if qsc and qsc_type == fmt and
+          qsc.size >= seq.length then
+        return qsc
+      end
+
+      # default output quality score type is :phred
+      fmt ||= :phred
+      # If quality score type of the sequence is nil, implicitly
+      # regarded as :phred.
+      qsc_type ||= :phred
+
+      # checks error_probabilities
+      ep = @sequence.error_probabilities
+      if ep and ep.size >= seq.length then
+        case fmt
+        when :phred
+          return Bio::Sequence::QualityScore::Phred.p2q(ep[0, seq.length])
+        when :solexa
+          return Bio::Sequence::QualityScore::Solexa.p2q(ep[0, seq.length])
+        end
+      end
+
+      # Checks if scores can be converted.
+      if qsc and qsc.size >= seq.length then
+        case [ qsc_type, fmt ]
+        when [ :phred, :solexa ]
+          return Bio::Sequence::QualityScore::Phred.convert_scores_to_solexa(qsc[0, seq.length])
+        when [ :solexa, :phred ]
+          return Bio::Sequence::QualityScore::Solexa.convert_scores_to_phred(qsc[0, seq.length])
+        end
+      end
+
+      # checks quality scores type
+      case qsc_type
+      when :phred, :solexa
+        #does nothing
+      else
+        qsc_type = nil
+        qsc = nil
+      end
+
+      # collects piece of information
+      qsc_cov = qsc ? qsc.size.quo(seq.length) : 0
+      ep_cov = ep ? ep.size.quo(seq.length) : 0
+      if qsc_cov > ep_cov then
+        case [ qsc_type, fmt ]
+        when [ :phred, :phred ], [ :solexa, :solexa ]
+          return qsc
+        when [ :phred, :solexa ]
+          return Bio::Sequence::QualityScore::Phred.convert_scores_to_solexa(qsc)
+        when [ :solexa, :phred ]
+          return Bio::Sequence::QualityScore::Solexa.convert_scores_to_phred(qsc)
+        end
+      elsif ep_cov > qsc_cov then
+        case fmt
+        when :phred
+          return Bio::Sequence::QualityScore::Phred.p2q(ep)
+        when :solexa
+          return Bio::Sequence::QualityScore::Solexa.p2q(ep)
+        end
+      end
+
+      # if no information, returns empty array
+      return []
+    end
+  end #class Qual
+
+end #module Bio::Sequence::Format::Formatter
+