From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 27 Jan 2012 13:09:20 +0000 (+0000)
Subject: final touches to align.rb
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=64d9b883ac41c0e7263aed9d30bd302615764776;p=biopieces.git

final touches to align.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1735 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/align.rb b/code_ruby/lib/maasha/align.rb
index 411e459..cc38a83 100755
--- a/code_ruby/lib/maasha/align.rb
+++ b/code_ruby/lib/maasha/align.rb
@@ -29,18 +29,19 @@ require 'maasha/fasta'
 
 class AlignError < StandardError; end;
 
-CONSENSUS   = 20
+CONSENSUS   = 0.20
 INDEL_RATIO = 0.5
-QUAL_MIN    = 15
+FREQ_MIN    = 2
 QUAL_BASE   = 64
 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
 BIT_W = BIT_A | BIT_T
@@ -91,6 +92,8 @@ end
 
 # Class for aligning sequences.
 class Align
+  attr_reader :entries
+
   # Class method to align sequences in a list of Seq objects and
   # return these as a new list of Seq objects.
   def self.muscle(entries, verbose = false)
@@ -124,26 +127,59 @@ class Align
       end
     end
 
-    result
+    self.new(result)
+  end
+
+  # Method to initialize an Align object with a list of aligned Seq objects.
+  def initialize(entries)
+    @entries = entries
+  end
+
+  # Method that returns the length of the alignment.
+  def length
+    @entries.first.length
+  end
+
+  # Method that returns the number of members or sequences in the alignment.
+  def members
+    @entries.size
   end
 
-  # Class method to create a consensus sequence from a list of Seq objects and
+  # Method to create a consensus sequence from an Align object and
   # return a new Seq object with the consensus.
-  def self.consensus(entries)
-    cons = Consensus.new(entries.first.length)
+  def consensus
+    cons = Consensus.new(self.length)
 
-    entries.each { |entry| cons.add(entry) }
+    @entries.each { |entry| cons.add(entry) }
 
     cons.to_seq
   end
 
+  # Method to pretty print an alignment from an Align object.
+  def to_s
+    cons = self.consensus
+    cons.mask_seq_soft!(20) unless cons.qual.nil?
+
+    max_name = @entries.group_by { |entry| entry.seq_name.length }.max.first
+
+    @entries.each do |entry|
+      puts 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?
+    output
+  end
+
+  private
+
   class Consensus
     # Method to initialize a Consensus object given a Seq object, which is added
     # to the Consensus.
     def initialize(length)
       @length = length
        
-      @count    = NArray.int(@length)
       @freq     = NArray.int(@length, ALPH_DNA.size)
       @qual     = NArray.int(@length, ALPH_DNA.size)
       @mask_A   = NArray.byte(@length).fill!(BIT_A)
@@ -151,13 +187,14 @@ class Align
       @mask_C   = NArray.byte(@length).fill!(BIT_C)
       @mask_G   = NArray.byte(@length).fill!(BIT_G)
       @has_qual = false
+      @count    = 0
     end
 
     # Method to add a Seq entry to a Consensus object.
     def add(entry)
-      seq  = NArray.to_na(entry.seq.downcase.tr(TR_NUC, TR_HEX), "byte")
+      @count += 1
 
-      @count += seq > 0
+      seq = NArray.to_na(entry.seq.downcase.tr(TR_NUC, TR_HEX), "byte")
 
       mask_A = (seq & @mask_A) > 0
       mask_T = (seq & @mask_T) > 0
@@ -182,7 +219,6 @@ class Align
     end
 
     def to_seq
-      #qual_filter
       new_seq      = Seq.new
       new_seq.seq  = consensus_seq
       new_seq.qual = consensus_qual if @has_qual
@@ -193,58 +229,30 @@ class Align
 
     private
 
-    # Method that calculates the sum for each column except the indel row and
-    # returns the sum in an NArray.
-    def freq_total
-      @freq.sum(1)
-    end
-
-    # Method that locates the maximum value for each column and
-    # returns this in an NArray.
-    def freq_max
-      @freq.max(1)
-    end
-
-    def qual_mean
-      freq = @freq[true, [0 ... ALPH_DNA.size]]
-      @qual / (freq + freq.eq(0))
-    end
-
-    def freq_percent
-      (@freq / freq_total.to_type("float") * 100).round
-    end
-
     # Method to calculate a consensus sequence from a Consensus object.
     def consensus_seq
-      fp    = freq_percent > CONSENSUS
+      fp = (@freq.to_type("float") / @count) > CONSENSUS
+
+      fp *= @freq >= FREQ_MIN
+
       cons  = NArray.byte(@length)
       cons |= fp[true, ROW_A] *= BIT_A
       cons |= fp[true, ROW_T] *= BIT_T
       cons |= fp[true, ROW_C] *= BIT_C
       cons |= fp[true, ROW_G] *= BIT_G
-
-      cons *= @count > @count.max * INDEL_RATIO
+#      cons *= @freq.sum(1).to_type("float") / @count > INDEL_RATIO
 
       cons.to_s.tr!(TR_HEX, TR_NUC).upcase
     end
 
     def consensus_qual
-      q = (@qual / (@count + @count.eq(0))).max(1)
+      q = qual_mean.max(1)
 
       (q.to_type("byte") + QUAL_BASE).to_s
     end
 
-    def qual_filter
-      filter = qual_mean > QUAL_MIN
-
-  #    pp @freq
-  #    pp @qual
-
-  #    @freq *= filter
-  #    @qual *= filter
-
-  #    pp @freq
-  #    pp @qual
+    def qual_mean
+      @qual / (@freq + @freq.eq(0))
     end
   end
 end