X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=code_ruby%2Flib%2Fmaasha%2Falign.rb;h=c139fe8d89c30a773df458f23e730d2a73e992c4;hb=c4b49c5ce1ed3b46ae37e6ebd73c21d67d6d4810;hp=f7f59f6b265f911f833a740ad4d4a782cdfc3a37;hpb=df43a5627df2505bf5fc913aa564a7f6428f82b2;p=biopieces.git

diff --git a/code_ruby/lib/maasha/align.rb b/code_ruby/lib/maasha/align.rb
index f7f59f6..c139fe8 100755
--- a/code_ruby/lib/maasha/align.rb
+++ b/code_ruby/lib/maasha/align.rb
@@ -25,21 +25,19 @@
 require 'pp'
 require 'open3'
 require 'narray'
+require 'maasha/align/pair'
 require 'maasha/fasta'
 
 class AlignError < StandardError; end;
 
-CONSENSUS   = 0.20
-FREQ_MIN    = 2
-QUAL_MIN    = 20
-ALPH_DNA    = %w{A T C G}
-ALPH_AMBI   = %w{A T C G M R W S Y K V H D B N}
+ALPH_DNA  = %w{A T C G}
+ALPH_AMBI = %w{A T C G M R W S Y K V H D B N}
 
 BIT_INDEL = 0
-# BIT_A = 1 << 0
-# BIT_T = 1 << 1
-# BIT_C = 1 << 2
-# BIT_G = 1 << 3
+BIT_A = 1 << 0
+BIT_T = 1 << 1
+BIT_C = 1 << 2
+BIT_G = 1 << 3
 
 BIT_M = BIT_A | BIT_C
 BIT_R = BIT_A | BIT_G
@@ -91,7 +89,10 @@ end
 
 # Class for aligning sequences.
 class Align
-  attr_reader :entries
+  attr_accessor :options
+  attr_reader   :entries
+
+  include PairAlign
 
   # Class method to align sequences in a list of Seq objects and
   # return these as a new list of Seq objects.
@@ -101,9 +102,9 @@ class Align
 
     Open3.popen3("muscle", "-quiet") do |stdin, stdout, stderr|
       entries.each do |entry|
-        raise AlignError, "Duplicate sequence name: #{entry.seq_name}" if index.has_key? entry.seq_name
+        raise AlignError, "Duplicate sequence name: #{entry.seq_name}" if index[entry.seq_name]
 
-        index[entry.seq_name] = entry
+        index[entry.seq_name] = entry.dup
 
         stdin.puts entry.to_fasta
       end
@@ -128,10 +129,22 @@ class Align
 
     self.new(result)
   end
+  
+  # Class method to create a pairwise alignment of two given Seq objects. The
+  # alignment is created by casting a search space the size of the sequences
+  # and save the best scoring match between the sequences and recurse into
+  # the left and right search spaced around this match. When all search spaces
+  # are exhausted the saved matches are used to insert gaps in the sequences.
+  def self.pair(q_entry, s_entry)
+    AlignPair.align(q_entry, s_entry)
+
+    self.new([q_entry, s_entry])
+  end
 
   # Method to initialize an Align object with a list of aligned Seq objects.
-  def initialize(entries)
+  def initialize(entries, options = {})
     @entries = entries
+    @options = options
   end
 
   # Method that returns the length of the alignment.
@@ -144,39 +157,68 @@ class Align
     @entries.size
   end
 
+  # Method that returns the identity of an alignment with two members.
+  def identity
+    if self.members != 2
+      raise AlignError "Bad number of members for similarity calculation: #{self.members}"
+    end
+
+    na1 = NArray.to_na(@entries[0].seq.upcase, "byte")
+    na2 = NArray.to_na(@entries[1].seq.upcase, "byte")
+
+    shared   = (na1 - na2).count_false
+    total    = (@entries[0].length < @entries[1].length) ? @entries[0].length : @entries[1].length
+    identity = shared.to_f / total
+
+    identity
+  end
+
   # Method to create a consensus sequence from an Align object and
   # return a new Seq object with the consensus.
   def consensus
-    cons = Consensus.new(@entries)
-    cons.to_seq
+    cons = Consensus.new(@entries, @options)
+    cons.consensus
   end
 
   # Method to pretty print an alignment from an Align object.
   def to_s
-    cons = self.consensus
-    cons.mask_seq_soft!(QUAL_MIN) unless cons.qual.nil?
+    cons = Consensus.new(@entries, @options)
+    cons.mask_entries!
 
     max_name = @entries.group_by { |entry| entry.seq_name.length }.max.first
 
+    output = ""
+
     @entries.each do |entry|
-      entry.mask_seq_soft!(QUAL_MIN) unless entry.qual.nil?
-      puts entry.seq_name + (" " * (max_name + 3 - entry.seq_name.length )) + entry.seq
+      output << entry.seq_name + (" " * (max_name + 3 - entry.seq_name.length )) + entry.seq + $/
     end
 
-    output = ""
-    output << " " * (max_name + 3) + cons.seq + $/
-    output << " " * (max_name + 3) + cons.qual.tr("[@-h]", "           ..........ooooooooooOOOOOOOOOO") unless cons.qual.nil?
+    cons_entry = cons.consensus 
+
+    output << " " * (max_name + 3) + cons_entry.seq
+    output << $/ + " " * (max_name + 3) + cons_entry.qual.tr("[@-h]", "           ..........ooooooooooOOOOOOOOOO") unless cons_entry.qual.nil?
     output
   end
 
+  # Method for iterating each of the aligned sequences.
+  def each
+    if block_given?
+      @entries.each { |entry| yield entry }
+    else
+      return @entries
+    end
+  end
+
   private
 
   class Consensus
     # Method to initialize a Consensus object given a list of aligned Seq object.
-    def initialize(entries)
+    def initialize(entries, options)
       @entries = entries
-      @cols    = entries.first.length
-      @rows    = entries.size
+      @options = options
+
+      @cols = entries.first.seq.length
+      @rows = entries.size
 
       @has_qual = entries.first.qual.nil? ? false : true
 
@@ -184,21 +226,28 @@ class Align
       @na_qual = NArray.byte(@cols, @rows) if @has_qual
 
       na_add_entries
+      consensus_calc
+    end
 
-      if @has_qual
-        m1 = mask_high_qual
-        m2 = mask_conserved_columns
-        m3 = mask_conserved_residues
+    # Method that lowercase residues that have been removed during
+    # the determination of the consensus sequence.
+    def mask_entries!
+      na_seq = NArray.byte(@cols, @rows)
+
+      @entries.each_with_index do |entry, i|
+        na_seq[true, i]  = NArray.to_na(entry.seq.upcase, "byte")
+      end
 
-        @na_seq  *= m3
-        @na_qual *= m3
+      na_seq += ((na_seq.ne('-'.ord) - @na_seq.ne(0)) * ' '.ord)
 
-        @na_seq  *= (m1 | m2)
-        @na_qual *= (m1 | m2)
+      @entries.each_with_index do |entry, i|
+        entry.seq = na_seq[true, i].to_s
       end
     end
 
-    def to_seq
+    # Method that returns a Sequence object with a consensus sequence
+    # for the entries in an Align object.
+    def consensus
       new_seq      = Seq.new
       new_seq.seq  = consensus_seq
       new_seq.qual = consensus_qual if @has_qual
@@ -209,36 +258,110 @@ class Align
 
     private
 
+    # Method to add a Seq entry object to the two NArrays; @na_seq and @na_qual
     def na_add_entries
       @entries.each_with_index do |entry, i|
         @na_seq[true, i]  = NArray.to_na(entry.seq.downcase.tr(TR_NUC, TR_HEX), "byte")
-        @na_qual[true, i] = NArray.to_na(entry.qual, "byte") - SCORE_ILLUMINA if @has_qual
+        @na_qual[true, i] = NArray.to_na(entry.qual, "byte") - Seq::SCORE_BASE if @has_qual
       end
     end
 
-    def mask_high_qual
-      @na_qual > QUAL_MIN
+    # Method to calculate a consensus sequence from a list of sequenced stored in two
+    # NArrays.
+    def consensus_calc
+      if @has_qual
+        if @options[:quality_min]
+          mask = mask_quality_min
+
+          @na_seq  *= mask
+          @na_qual *= mask
+        end
+
+        if @options[:quality_mean]
+          mask = mask_quality_mean
+
+          @na_seq  *= mask
+          @na_qual *= mask
+        end
+      end
+
+      if @options[:sequence_min]
+        mask = mask_sequence_min
+
+        @na_seq  *= mask
+        @na_qual *= mask if @has_qual
+      end
+
+      if @options[:gap_max]
+        mask = mask_gap_max
+
+        @na_seq  *= mask
+        @na_qual *= mask if @has_qual
+      end
+
+      if @options[:residue_min]
+        mask = mask_residue_min
+
+        @na_seq  *= mask
+        @na_qual *= mask if @has_qual
+      end
     end
 
-    def mask_conserved_columns
-      @na_seq * (@na_seq - @na_seq[true, 0]).sum(1).eq(0) > 0
+    # Mask that indicates which columns have more than sequence_min sequences.
+    # Columns with less than sequence_min are 0'ed, otherwise set to 1.
+    def mask_sequence_min
+      mask  = NArray.byte(@cols, @rows) + 1
+      mask *= ((@na_seq > 0).to_type("int").sum(1) >= @options[:sequence_min])
+      mask
     end
 
-    def mask_conserved_residues
-      factor = (1 / @rows.to_f)
-      mask_A = @na_seq & BIT_A > 0
-      mask_T = @na_seq & BIT_T > 0
-      mask_C = @na_seq & BIT_C > 0
-      mask_G = @na_seq & BIT_G > 0
+    # Mask that indicates which residue frequencies that are above the residue_min.
+    # The residue frequencies are calculated for each column and residue type as the
+    # number of each residue type over the sum of all non-gap residues in that column.
+    # Positions with residues above the residue_min are indicated with 1.
+    def mask_residue_min
+      cons_min = @options[:residue_min]
+      factor   = 1 / @na_seq.ne(0).to_type("float").sum(1)
 
-      mask_A = (mask_A * mask_A.sum(1)).to_f * factor > CONSENSUS
-      mask_T = (mask_T * mask_T.sum(1)).to_f * factor > CONSENSUS
-      mask_C = (mask_C * mask_C.sum(1)).to_f * factor > CONSENSUS
-      mask_G = (mask_G * mask_G.sum(1)).to_f * factor > CONSENSUS
+      mask_A = (@na_seq & BIT_A > 0).to_type("int")
+      mask_T = (@na_seq & BIT_T > 0).to_type("int")
+      mask_C = (@na_seq & BIT_C > 0).to_type("int")
+      mask_G = (@na_seq & BIT_G > 0).to_type("int")
+
+      mask_A = (mask_A * mask_A.sum(1)) * factor >= cons_min
+      mask_T = (mask_T * mask_T.sum(1)) * factor >= cons_min
+      mask_C = (mask_C * mask_C.sum(1)) * factor >= cons_min
+      mask_G = (mask_G * mask_G.sum(1)) * factor >= cons_min
 
       mask_A | mask_T | mask_C | mask_G
     end
 
+    # Mask that indicates which columns contain fewer gaps than max_gap.
+    # Columns with more gaps are 0'ed, others are set to 1.
+    def mask_gap_max
+      mask  = NArray.byte(@cols, @rows) + 1
+      mask *= @na_seq.ne(0).to_type("float").sum(1) / @rows > @options[:gap_max]
+
+      mask
+    end
+
+    # Mask that indicates which residues in an alignment are above quality_min.
+    # Positions with subquality are 0'ed - all others are set to 1.
+    def mask_quality_min
+      @na_qual > @options[:quality_min]
+    end
+
+    # Mask that indicates which columns have a quality mean above quality_mean which
+    # is the mean of all non-gap quality residues in that column. Columns with less then
+    # quality_mean are 0'ed, otherwise set to 1.
+    def mask_quality_mean
+      mask     = NArray.byte(@cols, @rows) + 1
+      residues = @na_seq.ne(0).to_type("int").sum(1)
+      quality  = @na_qual.to_type("float").sum(1)
+
+      mask * (quality / residues).round > @options[:quality_mean]
+    end
+
     # Method to calculate a consensus sequence from a Consensus object.
     def consensus_seq
       cons  = NArray.byte(@cols)
@@ -252,16 +375,9 @@ class Align
 
     # Method to calculate a consensus quality from a Consensus object.
     def consensus_qual
-      (@na_qual.mean(1).round.to_type("byte") + SCORE_ILLUMINA).to_s
+      (@na_qual.mean(1).round.to_type("byte") + Seq::SCORE_BASE).to_s
     end
   end
 end
 
-
-
 __END__
-
-cons |= ((@na_seq & BIT_A > 0).sum(1).to_type("float") * (1 / @rows.to_f) > CONSENSUS) * BIT_A
-cons |= ((@na_seq & BIT_T > 0).sum(1).to_type("float") * (1 / @rows.to_f) > CONSENSUS) * BIT_T
-cons |= ((@na_seq & BIT_C > 0).sum(1).to_type("float") * (1 / @rows.to_f) > CONSENSUS) * BIT_C
-cons |= ((@na_seq & BIT_G > 0).sum(1).to_type("float") * (1 / @rows.to_f) > CONSENSUS) * BIT_G