Class: FrequencyTable

Inherits:
Object
  • Object
show all
Defined in:
lib/scbi_cominer/classes/frequency_table.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ FrequencyTable

Returns a new instance of FrequencyTable.



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 5

def initialize
  @frequency_table = {}
  @position_table = {}
  @sequences =[]
end

Instance Attribute Details

#frequency_table ⇒ Object

Returns the value of attribute frequency_table.



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 3

def frequency_table
  @frequency_table
end

#position_table ⇒ Object

Returns the value of attribute position_table.



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 3

def position_table
  @position_table
end

#sequences ⇒ Object

Returns the value of attribute sequences.



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 3

def sequences
  @sequences
end

Instance Method Details

#add_fasta(name, fasta, in_consensus_offset, align_clip_start, align_clip_end) ⇒ Object 



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 107

def add_fasta(name,fasta, in_consensus_offset, align_clip_start, align_clip_end)

  @sequences.push({:name=>name,:fasta=>fasta})
  index = @sequences.length
  
  fasta_u=fasta.upcase
  
  i = (align_clip_start.to_i+in_consensus_offset.to_i)-2
  
  # seq_i=in_seq_offset.to_i
  
  # while !(c=fasta_u[seq_i]).nil?
  # puts ("_"*i+fasta[align_clip_start.to_i-1..align_clip_end.to_i-1])[0..80]+'...'
  fasta[align_clip_start.to_i-1..align_clip_end.to_i-1].upcase.each_char do |c|

    #get current freq
    freq = @frequency_table[c]
    if freq.nil?
      @frequency_table[c] = []
      freq = @frequency_table[c]
    end

    #increment current freq
    if freq[i].nil?
      freq[i] = 1
    else
      freq[i]+=1
    end

    #get current pos
    pos = @position_table[c]
    if pos.nil?
      @position_table[c] = []
      pos = @position_table[c]
    end

    #increment current freq
    if pos[i].nil?
      pos[i] = [index]
    else
      pos[i].push index
    end

    #increment pos
    i +=1
  end

  #	puts "  "+fasta[0..30]
end

#add_read(read) ⇒ Object 



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 99

def add_read(read)
  add_fasta(read.name, read.fasta, read.start_in_consensus, read.align_clip_start, read.align_clip_end)
end

#add_sequence(seq, offset) ⇒ Object 



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 103

def add_sequence(seq, offset)
  add_fasta(seq.seq_name,seq.seq_fasta)
end

#consensus_freq(pos) ⇒ Object

cuenta las secuencias efectivas de la posicion pos



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 62

def consensus_freq(pos)
  ke=nil
  m = 0

  @frequency_table.each { |k,v|

    if (!v[pos].nil?) && (k!='-') && (k!='*')
      if v[pos] >= m
        m = v[pos]
        ke=k
      end

    end

  }

  return [ke,m]
  #return @sequences.count
end

#extract_col(pos) ⇒ Object 



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 157

def extract_col(pos)

  h={}

  @frequency_table.each do |k,v|

    if (!v[pos].nil?) && (k!='-') && (k!='*')
      if v[pos]>0
        h[k]=v[pos]
      end
    end

  end

  return h

end

#inspect ⇒ Object 



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 229

def inspect

  # return  @frequency_table.to_json
  
  res = ''

  @frequency_table.each do |c,v|

    res += c+':'+(v[0..30].map{|c1|  c1 ||= 0 }).join("")+"...more.\n"

  end

  @position_table.each do |c,v|

    #			res += c+':'+(v[0..10].map{|c1|  (c1 && ('['+c1.map{|c2| @sequences[c2-1].seq_name}.join(","))+']') || "[]" }).join(" - ")+"...more.\n"
    res += c+':'+(v[0..10].map{|c1|  (c1 && ('['+c1.map{|c2| @sequences[c2-1][:name]}.join(","))+']') || "[]" }).join(" - ")+"...more.\n"

  end

  return res

end

#inspect_pos(pos_start, pos_end) ⇒ Object 



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 252

def inspect_pos(pos_start,pos_end)


  res = ''

  @frequency_table.each do |c,v|

    res += c+':'+(v[pos_start..pos_end].map{|c1|  c1 ||= 0 }).join("")+"...more.\n"

  end

  return res
end

#max_length ⇒ Object 



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 83

def max_length
  m = 0
  mk = nil

  @frequency_table.each { |k,v|

    if v.length>m
      m = v.length
      mk = k
    end

  }

  return m
end

#max_length_key ⇒ Object 



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 11

def max_length_key
  m = 0
  mk = nil

  @frequency_table.each { |k,v|

    if v.length>m
      m = v.length
      mk = k
    end

  }

  return mk
end

#nseq(pos) ⇒ Object

cuenta las secuencias efectivas de la posicion pos



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 28

def nseq(pos)
  m = 0

  @frequency_table.each { |k,v|

    if (!v[pos].nil?) && (k!='-')
      #puts v[pos].to_s + k if pos==0
      m += v[pos]
    end

  }

  return m
  #return @sequences.count
end

#nseq_valid(pos) ⇒ Object

cuenta las secuencias efectivas de la posicion pos



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 45

def nseq_valid(pos)
  m = 0

  @frequency_table.each { |k,v|

    if (!v[pos].nil?) && (k!='-') && (k!='*')
      #puts v[pos].to_s + k if pos==0
      m += v[pos]
    end

  }

  return m
  #return @sequences.count
end

#valid_snp(pos) ⇒ Object 



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# File 'lib/scbi_cominer/classes/frequency_table.rb', line 175

def valid_snp(pos)
  res = false

  # a valid SNP is a change in at least two valid sequences.

  total_seqs = nseq_valid(pos)
  consensus_base, consensus_frequency = consensus_freq(pos)
  #	puts h.to_json
  # change a pos

  #if pos = 128
  #			@frequency_table['A'][pos]=1
  #			@frequency_table['C'][pos]=2
  #			@frequency_table['T'][pos]=0
  #			@frequency_table['G'][pos]=4
  #	end
  #
  if consensus_frequency <= total_seqs - 2

    h = extract_col(pos)



    h.each do |k,v|
      if (k!=consensus_base) && (v>=2)
        res = true
        #					puts "#{k} is #{v}>=2"
        break
      end
    end


  end

  #	puts inspect_pos(pos,pos)
  #	puts "POS: #{pos}"
  #	puts res.to_s
  #  puts "base #{consensus_base}, freq #{consensus_frequency}, tot: #{total_seqs}"
  #	puts '-' * 20

  #puts "nseq[#{pos}] =  #{total_seqs} => #{consensus_base}: #{consensus_frequency}"

  #	@frequency_table.each { |k,v|
  #
  #  		puts "#{k}:#{v[pos] ||= '0'}"
  #
  #
  #	}
  #
  #	puts res.to_s

  return res
end