Class: ExtractStats
- Inherits:
-
Object
- Object
- ExtractStats
- Defined in:
- lib/seqtrimnext/classes/extract_stats.rb
Instance Method Summary collapse
- #add_key(key) ⇒ Object
- #add_qv(q, i) ⇒ Object
- #extract_qv_from_sequence(qual) ⇒ Object
- #extract_stats_from_sequences(sequence_readers) ⇒ Object
- #get_max_key ⇒ Object
-
#initialize(sequence_readers, params) ⇒ ExtractStats
constructor
A new instance of ExtractStats.
- #plot_lengths ⇒ Object
- #plot_qualities ⇒ Object
- #print_global_stats ⇒ Object
- #set_params_and_results ⇒ Object
Constructor Details
#initialize(sequence_readers, params) ⇒ ExtractStats
Returns a new instance of ExtractStats.
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# File 'lib/seqtrimnext/classes/extract_stats.rb', line 14 def initialize(sequence_readers,params) @sequence_lengths = [] #array of sequences lengths @length_frequency = [] #number of sequences of each size (frequency) @keys={} #found keys @params = params @use_qual=sequence_readers.first.with_qual? # @params.get_param('use_qual') @totalnt=0 @qv=[] @sequence_lengths_stats, @length_frequency_stats, @quality_stats = extract_stats_from_sequences(sequence_readers) 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 172 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 153 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 166 def extract_qv_from_sequence(qual) qual.each_with_index do |q,i| add_qv(q,i) end end |
#extract_stats_from_sequences(sequence_readers) ⇒ Object
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# File 'lib/seqtrimnext/classes/extract_stats.rb', line 40 def extract_stats_from_sequences(sequence_readers) sequence_readers.each do |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 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 180 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 76 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 110 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 213 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 184 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').to_s=='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 |