Class: StatsReport

Inherits:
Object
  • Object
show all
Defined in:
lib/seqtrimnext_report/classes/stats_report.rb

Instance Method Summary collapse

Constructor Details

#initialize(all_params, initial_stats, stats, plugin_nts_hash, output_folder, output_latex) ⇒ StatsReport

Returns a new instance of StatsReport.



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# File 'lib/seqtrimnext_report/classes/stats_report.rb', line 3

def initialize(all_params,initial_stats,stats,plugin_nts_hash,output_folder,output_latex)
  
  output2=File.open(File.join(output_latex,'stats.tex'), 'w')
  output2.puts "%!TEX root = FinalReport.tex"
  
  if (stats['sequences'].nil?) || (stats['sequences']['count'].nil?)
    puts "sequences info does not exist in stats.json\n"
    exit(-1)
  end
  
  input_seqs = stats['sequences']['count']['input_count'].to_i
  rejected_seqs = stats['sequences']['count']['rejected'].to_i
  output_seqs = stats['sequences']['count']['output_seqs'].to_i

  #------------------------------------------------------------------------------------------ solo cuando hay pareadas
  output_seqs_paired = 0
  total_output_seqs = 0

  if (!stats['sequences']['count']['output_seqs_paired'].nil?)
    output_seqs_paired = stats['sequences']['count']['output_seqs_paired'].to_i
    total_output_seqs = output_seqs_paired+output_seqs
  end
  #-------------------------------------------------------------------------------------------------------------------
  low_complex = 0
  if (!stats['sequences']['count']['output_seqs_low_complexity'].nil?)
    low_complex = stats['sequences']['count']['output_seqs_low_complexity'].to_i # solo cuando hay baja complejidad (no hay cuando es genomico)
  end
  # graph files ----------------------------------------------------
  
   # if File.exist?(File.join(output_latex,'graphs','size_stats.png'))
    output2.puts '\input{input_graph}'
   # end
  
   # if File.exist?(File.join(output_latex,'graphs','qualities.png'))
    output2.puts '\input{qv_graph}'
   # end
  
   # if File.exist?(File.join(output_latex,'graphs','PluginExtractInserts_insert_size.png'))
    output2.puts '\input{output_graph}'+"\n\n"
   # end
  #------------------------------------------------------------------
  
  (input_mode, output_mode) = get_mode(initial_stats,stats)
  (input_mean, output_mean) = get_mean(initial_stats,stats)
  
  #--------------------------------------------------------------------------- build table
  output2.puts '\begin{table}[H]'
  output2.puts '\begin{center}'
  output2.puts '\begin{tabular}{l r r}'
  output2.puts " \\hline"
  if (!input_seqs.nil?)
    output2.puts "Input reads: & total & #{input_seqs} \\\\"
  end
  if (!initial_stats['smallest_sequence_size'].nil?)
    output2.puts " & Smallest read (bp) & #{initial_stats['smallest_sequence_size'].to_i} \\\\"
  end
  if (!initial_stats['biggest_sequence_size'].nil?)
    output2.puts " & Largest read (bp)& #{initial_stats['biggest_sequence_size'].to_i} \\\\"
  end
  output2.puts " & Mode (bp) & #{input_mode} \\\\"
  output2.puts " & Mean (bp)& #{input_mean} \\\\"

  output2.puts " \\\\ \\hline"
  output2.puts "Output results: & total & #{output_seqs} \\\\"
  output2.puts " & Rejected & #{rejected_seqs} \\\\"
  if (low_complex != 0)
    output2.puts " & Low complexity reads & #{low_complex} \\\\"
  end
  output2.puts " & Mode (bp)& #{output_mode} \\\\"
  output2.puts " & Mean (bp)& #{output_mean} \\\\"
  
  #-------------------------------------------------- solo cuando hay pareadas
  output2.puts "\\\\"
  if (output_seqs_paired != 0)
    output2.puts " & Output paired reads & #{output_seqs_paired} \\\\"
    output2.puts " & Total output reads & #{total_output_seqs} \\\\"
    output2.puts "\\\\ \\hline"
    output2.puts "Linkers: & & \\\\"
    
    if (!stats['PluginLinker'].nil?)
      if (!stats['PluginLinker']['linker_id'].nil?)
        stats['PluginLinker']['linker_id'].each do |linker|
          output2.puts " & #{linker[0]} & #{linker[1]} \\\\"
        end
      end
      output2.puts "\\\\ \\hline"
      if (!stats['PluginLinker']['without_linker'].nil?)
        output2.puts "Without linkers: & total & #{stats['PluginLinker']['without_linker']['0']} \\\\"
      end
      
      output2.puts "\\\\ \\hline"
      output2.puts "Multiple linkers: & & \\\\"

      if (!stats['PluginLinker']['multiple_linker_id'].nil?)
        stats['PluginLinker']['multiple_linker_id'].each do |linker|
          output2.puts " & #{linker[0]} & #{linker[1]} \\\\"
        end
      end
      if (!stats['PluginLinker']['multiple_linker_count'].nil?)
        stats['PluginLinker']['multiple_linker_count'].each do |linker|
          output2.puts " & With #{linker[0]} linkers & #{linker[1]} \\\\"
        end
      end
    end
  end
  #--------------------------------------------------- end pareadas
  
  output2.puts "\\hline"
  
  output2.puts '\end{tabular}'
  output2.puts '\label{table:nonlin}'
  output2.puts '\end{center}'
  output2.puts '\end{table}'+"\n\n"
  #------------------------------------------------------------------------------- end table

  #-------------------------------------------------- MIDs
  if (!stats['PluginMids'].nil?) && (!stats['PluginMids']['mid_id'].nil?)
    mid_seqs = stats['PluginMids']['mid_id']['total']
    mid_seqs_percent = sprintf("%0.3f", (mid_seqs.to_f*100/input_seqs.to_f))
    output2.puts '\noindent \begin{minipage}{\linewidth}'
    output2.puts "number of reads with MID: #{mid_seqs} \(#{mid_seqs_percent}\\%\)"+'\\\\'+'\\\\'

    if (mid_seqs_percent.to_f <= 1)
      output2.puts '\fcolorbox{black}{yellow}{'+"\n"+'\begin{minipage}{\linewidth}{'+"\n"+'\textbf{WARNING: The number of reads with MID is so low that can be interpreted as a random finding. Your useful sequences are in the no\_MID folder, but you can also add any read classified as having a MID}'+"\n"+'}'+"\n"+'\end{minipage}'+"\n"+'}\\\\\\\\'
    end
    output2.puts '\end{minipage}'+"\n\n"
  end
  #----------------------------------------------------------------------------

  #------------------------------------------------------- make top five tables
  if !(stats['PluginVectors']).nil?
    if !(top_hash = stats['PluginVectors']['vectors_ids']).nil?
      make_a_top_five(output2, top_hash, 'Vectors')
    end
  end
  
  if !(stats['PluginAbAdapters']).nil?
    if !(top_hash = stats['PluginAbAdapters']['adapter_id']).nil?
      make_a_top_five(output2, top_hash, 'Adapters')
    end
  end
  
  if !(stats['PluginContaminants']).nil?
    if !(top_hash = stats['PluginContaminants']['contaminants_ids']).nil?
      make_a_top_five(output2, top_hash, 'Contaminants')
    end
  end
  #--------------------------------------------------------------------------
  
  # en las pareadas añadimos el inserto de izq y derecha ------------------------------------- solo cuando hay pareadas
  paired_nts=0
  if (stats['PluginExtractInserts']['left_insert_size'])
    stats['PluginExtractInserts']['left_insert_size'].each do |element|
      paired_nts += element[0].to_i*element[1].to_i
    end
  end
  if (stats['PluginExtractInserts']['right_insert_size'])
    stats['PluginExtractInserts']['right_insert_size'].each do |element|
      paired_nts += element[0].to_i*element[1].to_i
    end
  end
  #-------------------------------------------------------------------------------------------------------------------
  
  nts_total = initial_stats['nucleotide_count']
  print_trimmed_nts_stats_table(stats, output2, plugin_nts_hash,nts_total,paired_nts)
  
  output2.close

  puts "Statistic information was added to the report"
  
end

Instance Method Details

#get_mean(initial_stats, stats) ⇒ Object 



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# File 'lib/seqtrimnext_report/classes/stats_report.rb', line 203

def get_mean(initial_stats,stats)
  output_mean = 0

  # take the mean from initial_stats.json
  if (!initial_stats.nil? and !initial_stats.empty?)
    input_mean = sprintf("%0.1f", (initial_stats['mean_of_sequence_sizes']))
  else
    input_mean = 0
  end
    
  # calculate the mean using data from stats.json
  nts_count = 0
  seqs_count = 0
  if (!stats['PluginExtractInserts']['insert_size'].nil?)
    stats['PluginExtractInserts']['insert_size'].each do |key,value|
      seqs_count += value.to_i
      nts_count += (key.to_f*value)
    end
  
    if (nts_count == 0 || seqs_count == 0)
      output_mean = 0
    else
      output_mean = sprintf("%0.1f", (nts_count/seqs_count))
    end
  else
    output_mean = 0
  end
  
  return [input_mean, output_mean]
end

#get_mode(initial_stats, stats) ⇒ Object 



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# File 'lib/seqtrimnext_report/classes/stats_report.rb', line 175

def get_mode(initial_stats,stats)
  output_mode = 0
  mode_array = []
  
  # take the mode from initial_stats.json
  if (!initial_stats.nil? and !initial_stats.empty?)
    input_mode = initial_stats['mode_of_sizes']
  else
    input_mode = 0
  end
  
  # calculate the mode using data from stats.json
  if (!stats['PluginExtractInserts']['insert_size'].nil?)
    stats['PluginExtractInserts']['insert_size'].each do |key,value|
      mode_array[key.to_i]=value
    end
  
    mode_array.map!{|e| e || 0}
    s=ScbiStats.new(mode_array)
  
    output_mode = s.fat_mode
  else
    output_mode = 0
  end
  
  return [input_mode, output_mode]
end

#make_a_top_five(output2, top_hash, name) ⇒ Object 



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# File 'lib/seqtrimnext_report/classes/stats_report.rb', line 234

def make_a_top_five(output2,top_hash,name)
#-------------------------------------------------- build table
  output2.puts '\begin{table}[H]'
  output2.puts '\ccaption{'+"List of the most frequent~#{name}~found among your reads"+'}'
  output2.puts '\vspace{-0.5cm}'
  output2.puts '\begin{center}'
  output2.puts '\begin{tabular}{|p{11cm}|r|}'
  output2.puts '\hline'
  output2.puts "#{name} " +'& sequences \\\\ [0.5ex]'
  output2.puts '\hline'

  cont = 0
  top_hash.sort{|a,b| b[1]<=>a[1]}.each do |elem|
    tmp_name = elem[0].gsub('_','\_')
    output2.puts "#{tmp_name} \& #{elem[1]}"+'\\\\'
    cont+=1
    if (cont == 5)
      break
    end
  end

  output2.puts '\hline'
  output2.puts '\end{tabular}'
  output2.puts '\end{center}'
  # output2.puts '\label{table:top5}'
  output2.puts '\end{table}'+"\n\n"
#-------------------------------------------------- end table
end

#print_trimmed_nts_stats_table(stats, output2, plugin_nts_hash, nts_total, paired_nts) ⇒ Object 



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# File 'lib/seqtrimnext_report/classes/stats_report.rb', line 263

def print_trimmed_nts_stats_table(stats, output2, plugin_nts_hash, nts_total,paired_nts)

  nts_table_hash = {}
  insert_array = []
  warning_array = []
  
  plugin_nts_hash.each do |plugin|
    
    my_name = plugin[0]
    plugin_name = plugin[1]['plugin']
    plugin_field = plugin[1]['field']
    plugin_msg = plugin[1]['msg']
    plugin_threshold = plugin[1]['threshold']
    plugin_warning = plugin[1]['warning']
    
    if (!stats[plugin_name].nil?)
      if (!stats[plugin_name][plugin_field].nil?)
          
        count = 0
        stats[plugin_name][plugin_field].each do |element|
          count += element[0].to_i*element[1].to_i
        end
        
        if (plugin_name == 'PluginExtractInserts') && (plugin_field == 'insert_size') && (paired_nts > 0)
          count += paired_nts
        end
        
        my_percent = sprintf("%0.3f", (count.to_f*100/nts_total.to_f))
      
        if (plugin_name == 'PluginExtractInserts')
          if (my_percent.to_f <= plugin_threshold)
            plugin_msg.gsub!('my_percent',"#{my_percent}")
            insert_array.push '\noindent \fcolorbox{black}{pink}{'+"\n"+'\begin{minipage}{\linewidth}{'+"\n"+'\textbf{'+"#{plugin_warning}  #{plugin_msg}"+'}'+"\n"+'}'+"\n"+'\end{minipage}'+"\n"+'}\\\\\\\\'
          else
            plugin_warning = 'OK'
          end
        else
          if (my_percent.to_f >= plugin_threshold)
            plugin_msg.gsub!('my_percent',"#{my_percent}")
            warning_array.push '\noindent \fcolorbox{black}{yellow}{'+"\n"+'\begin{minipage}{\linewidth}{'+"\n"+'\textbf{'+"#{plugin_warning}  #{plugin_msg}"+'}'+"\n"+'}'+"\n"+'\end{minipage}'+"\n"+'}\\\\\\\\'
          else
            plugin_warning = 'OK'
          end
        end
      
        nts_table_hash[plugin_field] = ["#{my_name}&#{count}&#{my_percent} \\%&#{plugin_warning}\\\\",my_percent]
      
        # puts "#{plugin_name} #{plugin_field} #{count}"
      end
    end
  end
  
#-------------------------------------------------- build table
  output2.puts '\begin{table}[H]'
  output2.puts '\ccaption{Summary of nucleotides removed in every plugin.}'
  output2.puts '\begin{center}'
  output2.puts '\begin{tabular}{l r r c}'
  output2.puts '\hline'
  output2.puts 'Plugin & Nucleotides & Percent & Warnings \\\\ [0.5ex]'
  output2.puts '\hline'

  #the hash of hashes is ordered by value (number of sequences rejected)
  nts_table_ordered = nts_table_hash.sort {|a,b| b[1][1].to_i<=>a[1][1].to_i}

  nts_table_ordered.each do |element|
    if (element[0] != 'insert_size')
      output2.puts element[1][0]
    end
  end
  
  output2.puts '\hline'
  if (!nts_table_hash['insert_size'].nil?)
    output2.puts nts_table_hash['insert_size'][0]
  end
  output2.puts '\hline'
  output2.puts '\end{tabular}'
  output2.puts '\label{table:nonlin}'
  output2.puts '\end{center}'
  output2.puts '\end{table}'+"\n\n"
#-------------------------------------------------- end table

  output2.puts '\noindent \begin{minipage}{\textwidth}'
  
  output2.puts insert_array.join("\n")
  output2.puts warning_array.join("\n")
  
  output2.puts '\end{minipage}'+"\n\n"
  
end