Class: CONSENSUS::Sequences

Inherits:
Object
  • Object
show all
Defined in:
lib/most_frequent_seq.rb

Class Method Summary collapse

Class Method Details

.calcConsensus(seqs) ⇒ Object 



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# File 'lib/most_frequent_seq.rb', line 39

def self.calcConsensus(seqs)
    seql = seqs[0].length - 1
    seqr = ""

    #loop through each base index
    for i in 0..seql

      #establish array for counting bases at i position
      bases = [0,0,0,0,0,0,0] # A,G,C,T,N,-,U
      
      #for each seq, count the type of base at each index
      seqs.each { |n| 
        n = n.upcase
        if(n[i]=='A')
          bases[0] = bases[0]+1
        end
        if(n[i]=='G')
          bases[1] = bases[1]+1
        end
        if(n[i]=='C')
          bases[2] = bases[2]+1
        end
        if(n[i]=='T')
          bases[3] = bases[3]+1
        end
        if(n[i]=='N')
          bases[4] = bases[4]+1
        end
        if(n[i]=='-')
          bases[5] = bases[5]+1
        end
        if(n[i]=='U')
          bases[6] = bases[6]+1
        end
        
        }
      
      #find the max frequency , most frequent base at this index
      cb = bases.each_with_index.max[1]

      #convert back to string
      if(cb==0)
        base = 'A'
      end
      if(cb==1)
        base = 'G'
      end
      if(cb==2)
        base = 'C'
      end
      if(cb==3)
        base = 'T'
      end
      if(cb==4)
        base = 'N'
      end
      if(cb==5)
        base = '-'
      end
      if(cb==6)
        base = 'U'
      end
      
      #concat base to our consensus sequence
      seqr.concat(base.to_s)
         
      
      end
    return seqr
end