Class: Transfuse::Consensus

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(verbose) ⇒ Consensus

Returns a new instance of Consensus.



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# File 'lib/transfuse/consensus.rb', line 11

def initialize verbose
  @verbose = verbose
end

Instance Attribute Details

#contigs ⇒ Object (readonly)

Returns the value of attribute contigs.



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# File 'lib/transfuse/consensus.rb', line 9

def contigs
  @contigs
end

Instance Method Details

#count_exons(list) ⇒ Object 



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# File 'lib/transfuse/consensus.rb', line 15

def count_exons list
  exon_counts = {}
  list.each_with_index do |hash, index|
    seq = hash[:seq]
    exon_count=0
    gap_count=0
    prev=""
    seq.each_char do |c|
      if c=="-"
        base = "-"
      else
        base = "*"
      end

      if base!=prev
        if c=="-"
          gap_count+=1
        else
          exon_count+=1
        end
      end

      if c=="-"
        prev = "-"
      else
        prev = "*"
      end
    end
    exon_counts[exon_count] ||= []
    exon_counts[exon_count] << index
  end
  return exon_counts
end

#run(msa, scores, output) ⇒ Object 



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# File 'lib/transfuse/consensus.rb', line 49

def run msa, scores, output
  preoutput = "#{File.basename(output, File.extname(output))}_cons.fa"
  return preoutput if File.exist?(preoutput)
  print "writing consensus " if @verbose
  # msa is a hash
  #   key = cluster id
  #   value = list
  #     list of sequences in cluster aligned with gaps
  count = 0
  File.open("#{output}.data", "w") do |out2|
    File.open(preoutput, "w") do |out|
      msa.each do |id, seq_list|
        count+=1
        print "." if count%5_000==0 and @verbose
        exons={}
        cons = {}
        length = seq_list[0][:seq].length
        exons = count_exons(seq_list)

        exons.each do |count, list|
          0.upto(length-1) do |pos|
            base = "N"
            list.each do |index|
              b = seq_list[index][:seq][pos]
              if b != "-" and b != "N"
                base = b
              end
            end
            if base != "N"
              cons[count]||=""
              cons[count]<<base
            end
          end
        end

        cons.each_with_index do |s, index|
          out.write ">contig#{id}.#{index+1}\n"
          out.write "#{s[1]}\n"
        end

      end # msa.each
    end # file
  end # file open
  puts " Done" if @verbose
  return preoutput
end