Class: ExtractStats

Inherits:
Object
  • Object
show all
Defined in:
lib/seqtrimnext/classes/extract_stats.rb

Instance Method Summary collapse

Constructor Details

#initialize(sequence_reader, params) ⇒ ExtractStats

Returns a new instance of ExtractStats.



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# File 'lib/seqtrimnext/classes/extract_stats.rb', line 14

def initialize(sequence_reader,params)

  @sequence_lengths = []         #array of sequences lengths
  @length_frequency = []      #number of sequences of each size (frequency)
  @keys={}  #found keys
  @params = params
  @use_qual=sequence_reader.with_qual?
  # @params.get_param('use_qual')

  @totalnt=0
  @qv=[]


  @sequence_lengths_stats, @length_frequency_stats, @quality_stats = extract_stats_from_sequences(sequence_reader)


  set_params_and_results

  plot_lengths

  plot_qualities if @use_qual

  print_global_stats

end

Instance Method Details

#add_key(key) ⇒ Object 



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# File 'lib/seqtrimnext/classes/extract_stats.rb', line 169

def add_key(key)
  if @keys[key].nil?
   @keys[key]=1
  else
   @keys[key]+=1
  end
end

#add_qv(q, i) ⇒ Object 



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# File 'lib/seqtrimnext/classes/extract_stats.rb', line 150

def add_qv(q,i)
  if !@qv[i]
    @qv[i]={:max => 0, :min => 1000000, :nseq => 0, :tot => 0}
  end
  
  # set max
  @qv[i][:tot]+=q
  @qv[i][:nseq]+=1
  @qv[i][:min]=[@qv[i][:min],q].min
  @qv[i][:max]=[@qv[i][:max],q].max
  
end

#extract_qv_from_sequence(qual) ⇒ Object 



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# File 'lib/seqtrimnext/classes/extract_stats.rb', line 163

def extract_qv_from_sequence(qual)
  qual.each_with_index do |q,i|
    add_qv(q,i)
  end
end

#extract_stats_from_sequences(sequence_reader) ⇒ Object 



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# File 'lib/seqtrimnext/classes/extract_stats.rb', line 40

def extract_stats_from_sequences(sequence_reader)

  sequence_reader.each do |name_seq,fasta_seq,qual|
    l = fasta_seq.length

    @totalnt+=l

    #save all lengths
    @sequence_lengths.push l

    # add key value
    add_key(fasta_seq[0..3].upcase)

    # add fasta length
    @length_frequency[fasta_seq.length] = (@length_frequency[fasta_seq.length] || 1 ) + 1

    #extract qv values
    extract_qv_from_sequence(qual) if @use_qual

    # print some progress info
    if (sequence_reader.num_seqs % 10000==0)
      puts "Calculating stats: #{sequence_reader.num_seqs}"
    end

  end

  length_stats = ScbiNArray.to_na(@sequence_lengths)
  length_frequency_stats = ScbiNArray.to_na(@length_frequency.map{|e| e || 0})
  quality_stats = ScbiNArray.to_na(@qv) if @use_qual

  return [length_stats, length_frequency_stats, quality_stats]
end

#get_max_key ⇒ Object 



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# File 'lib/seqtrimnext/classes/extract_stats.rb', line 177

def get_max_key
  return @keys.keys.sort{|e1,e2| @keys[e1]<=>@keys[e2]}.last
end

#plot_lengths ⇒ Object 



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# File 'lib/seqtrimnext/classes/extract_stats.rb', line 73

def plot_lengths

  ## PLOT RESULTS
  if !File.exists?('graphs')
  	Dir.mkdir('graphs')
  end
  

  x = []
  y = []

  x =(0..@length_frequency.length-1).collect.to_a
  y = @length_frequency.map{|e| e || 0}

  file_name = 'graphs/size_stats.png'

  p=ScbiPlot::Lines.new(file_name,'Stats of sequence sizes')
  p.x_label= "Sequence length"
  p.y_label= "Number of sequences"

  p.add_x(x)

  p.add_series('sizes', y,'impulses',2)

  p.add_vertical_line('Mode',@length_frequency_stats.fat_mode[0])

  p.add_vertical_line('L',@params.get_param('min_sequence_size_raw').to_i)
  p.add_vertical_line('H',@params.get_param('max_sequence_size_raw').to_i)

  p.do_graph


end

#plot_qualities ⇒ Object 



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# File 'lib/seqtrimnext/classes/extract_stats.rb', line 107

def plot_qualities

  if !File.exists?('graphs')
  	Dir.mkdir('graphs')
  end
  minimum_qual_value = @params.get_param('min_quality').to_i
  
  # get qualities values
  x=[]
  y=[]
  min=[]
  max=[]
  qual_limit=[]

  @qv.each_with_index do |e,i|
    x << i
    y << (e[:tot]/e[:nseq])
    min << (e[:min])
    max << (e[:max])
    qual_limit << minimum_qual_value
      # puts "#{i}: #{e[:tot]/e[:nseq]}"
    end

  # make plot of qualities

  file_name='graphs/qualities.png'

	 p=ScbiPlot::Lines.new(file_name,'Stats of sequence qualities')
   p.x_label= "Nucleotide position"
   p.y_label= "Quality value"

    p.add_x(x)

    p.add_series('mean', y)
    p.add_series('min', min)
    p.add_series('max', max)
    p.add_series('qual limit',qual_limit)


    p.do_graph
end

#print_global_stats ⇒ Object 



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# File 'lib/seqtrimnext/classes/extract_stats.rb', line 210

def print_global_stats

if !@sequence_lengths_stats.nil?
initial_stats={}
initial_stats[:sequence_count] = @sequence_lengths_stats.size
initial_stats[:smallest_sequence_size] = @sequence_lengths_stats.min
initial_stats[:biggest_sequence_size] = @sequence_lengths_stats.max

initial_stats[:min_sequence_size_raw]=@params.get_param('min_sequence_size_raw')
initial_stats[:max_sequence_size_raw]=@params.get_param('max_sequence_size_raw')
initial_stats[:coefficient_of_variance]=@sequence_lengths_stats.variance_coefficient
initial_stats[:nucleotide_count]=@totalnt
initial_stats[:mode_of_sizes]=@length_frequency_stats.fat_mode[0]
initial_stats[:mean_of_sequence_sizes]=@sequence_lengths_stats.mean

initial_stats[:qv]=@qv
initial_stats[:used_key]=get_max_key
initial_stats[:all_keys]=@keys

File.open(File.join(OUTPUT_PATH,'initial_stats.json'),'w') do |f|
  f.puts JSON.pretty_generate(initial_stats)
end

puts "_"*10+ " STATISTICS "+"_"*10
puts "Total sequence count: #{@sequence_lengths_stats.size}"

puts "Smallest sequence: #{initial_stats[:smallest_sequence_size]} nt"
puts "Biggest sequence : #{initial_stats[:biggest_sequence_size]} nt"
puts "Mean of sequence sizes : #{initial_stats[:mean_of_sequence_sizes]} nt"
puts "Mode of sequence sizes : #{initial_stats[:mode_of_sizes]} nt"

puts "Low size limit : #{initial_stats[:min_sequence_size_raw]} nt"
puts "High size limit : #{initial_stats[:max_sequence_size_raw]} nt"

puts "Coefficient of variation: #{initial_stats[:coefficient_of_variance]} %"
puts "Total nucleotide count: #{initial_stats[:nucleotide_count]} nt"

puts "_"*30


end

end

#set_params_and_results ⇒ Object 



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# File 'lib/seqtrimnext/classes/extract_stats.rb', line 181

def set_params_and_results

  if @sequence_lengths.empty? 
    puts "No sequences has been sucessfully readed " 
    return
  end
  
  
  # set limiting parameters
  
  @params.set_param('sequencing_key',get_max_key)
  @params.set_param('all_found_keys',@keys.to_json)

  # sequence min size, is taken directly from params file
  # max sequence limit is calculated here 
  if (@sequence_lengths_stats.variance_coefficient<=10) or (@params.get_param('accept_very_long_sequences')=='true')

    # high size limit is calculated with stats
    @params.set_param('max_sequence_size_raw',(@sequence_lengths_stats.max+10).to_i)

  else # > 10 %

    # high size limit is calculated with stats
    @params.set_param('max_sequence_size_raw',(@sequence_lengths_stats.mean+2*@sequence_lengths_stats.stddev).to_i)
  end


end