Class: RejectedReport

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

Instance Method Summary collapse

Constructor Details

#initialize(stats, plugin_fix_hash, output_files, output_latex) ⇒ RejectedReport

Returns a new instance of RejectedReport.



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

def initialize(stats,plugin_fix_hash,output_files, output_latex)

  # write_plugin_json

  output3=File.open(File.join(output_latex,'rejected.tex'), 'w')
  output3.puts "%!TEX root = FinalReport.tex\n\n"

  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

  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 # solo cuando hay pareadas
    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 # no hay cuando es genomico
  end

  rejected_hash = {}
  data_hash = {}

  data_hash['value'] = rejected_seqs
  data_hash['warning'] = 'OK'
  data_hash['warning_msg'] = ''
  data_hash['percent'] = sprintf("%0.3f", (rejected_seqs.to_f*100/input_seqs.to_f))
  rejected_hash['rejected']=data_hash

  if (!stats['sequences']['rejected'].nil?)
    rejected_hash2 = load_plugins_info(stats, rejected_hash, input_seqs, plugin_fix_hash)
    #-------------------------------------------------- build table
    output3.puts '\begin{table}[H]'
    output3.puts '\begin{center}'
    output3.puts '\begin{tabular}{r r}'

    output3.puts "Input sequences & #{input_seqs}\\\\"
    output3.puts "Output sequences & #{output_seqs}\\\\"
    output3.puts "Rejected sequences & #{rejected_seqs}\\\\"
    if (output_seqs_paired != 0)
      output3.puts "Output paired sequences & #{output_seqs_paired} \\\\"
      output3.puts "Total output sequences & #{total_output_seqs} \\\\"
    end
    if (low_complex != 0)
      output3.puts "Low complexity sequences & #{low_complex} \\\\"
    end

    output3.puts '\end{tabular}'
    output3.puts '\label{table:input_seqs}'
    output3.puts '\end{center}'
    output3.puts '\end{table}'+"\n\n"
    #-------------------------------------------------- end table

    #-------------------------------------------------- build table
    output3.puts '\begin{table}[H]'
    output3.puts '\caption{Summary of reads removed in every plugin.}'
    output3.puts '\begin{center}'
    output3.puts '\begin{tabular}{l r r c}'
    output3.puts '\hline'
    output3.puts 'Case & Number of sequences & Percent & Warnings \\\\ [0.5ex]'
    output3.puts '\hline'

    #the hash of hashes is ordered by value (number of sequences rejected)
    rejected_ordered = rejected_hash2.sort {|a,b| b[1]['value']<=>a[1]['value']}

    rejected_ordered.each do |plugin|

      my_name = plugin[1]['name']
      my_value = plugin[1]['value']
      my_percent = plugin[1]['percent']
      my_warning = plugin[1]['warning']

      output3.puts "#{my_name}&#{my_value}&#{my_percent} \\%&#{my_warning}\\\\"
    end

    output3.puts '\hline'
    output3.puts "Total rejected&#{rejected_hash['rejected']['value']}&#{rejected_hash['rejected']['percent']} \\%&#{rejected_hash['rejected']['warning']}\\\\ [1ex]"
    output3.puts '\hline'
    output3.puts '\end{tabular}'
    output3.puts '\end{center}'
    output3.puts '\label{table:reads_removed}'
    output3.puts '\end{table}'+"\n\n"
    #-------------------------------------------------- end table

    rejected_ordered.each do |plugin|
      if (plugin[1]['warning'] != 'OK')
			if (!rejected_hash2[plugin[0]].nil?)
         plugin[1]['warning_msg'].gsub!('my_percent',"#{rejected_hash2["#{plugin[0]}"]['percent']}")
         output3.puts '\noindent\fcolorbox{black}{yellow}{'+"\n"+'\begin{minipage}{\linewidth}{'+"\n"+'\textbf{'+"#{plugin[1]['warning']}   #{plugin[1]['warning_msg']}"+'}'+"\n"+'}'+"\n"+'\end{minipage}'+"\n"+'}\\\\\\\\'
			end
      end
    end
  else
    output3.puts 'There are not rejected sequences\\\\'
  end

  output3.close

  puts "Information about rejected sequences was added to the report"
end

Instance Method Details

#load_plugins_info(stats, rejected_hash, input_seqs, plugin_fix_hash) ⇒ Object 



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# File 'lib/seqtrimnext_report/classes/rejected_report.rb', line 106

def load_plugins_info(stats, rejected_hash, input_seqs, plugin_fix_hash)
  data_hash = {}

  stats['sequences']['rejected'].each do |rejected|
    data_hash = {}
    if plugin_fix_hash[rejected[0]]
      data_hash['name'] = plugin_fix_hash[rejected[0]]['name']
      data_hash['value'] = rejected[1]
      data_hash['warning'] = 'OK'
      data_hash['warning_msg'] = ''
      data_hash['percent'] = sprintf("%0.3f", (rejected[1].to_f*100/input_seqs.to_f))
      rejected_hash[rejected[0]]=data_hash
    end
  end

  rejected_hash.each_key do |key|
    if (rejected_hash[key]['percent'].to_f >= plugin_fix_hash[key]['threshold'] )
      rejected_hash[key]['warning'] = plugin_fix_hash[key]['warning']
      rejected_hash[key]['warning_msg'] = plugin_fix_hash[key]['msg']
    end
  end
  return rejected_hash
end

#write_plugin_json ⇒ Object 



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# File 'lib/seqtrimnext_report/classes/rejected_report.rb', line 130

def write_plugin_json

  plugin_fix_hash = {}
  msgs_hash = {}

  msgs_hash['msg'] = "Warning!, there are a my_percent \\% of repeated sequences"
  msgs_hash['threshold'] = 9
  msgs_hash['warning'] = 'W1'

  plugin_fix_hash['repeated'] = msgs_hash
  msgs_hash = {}

  msgs_hash['msg'] = "Warning!, a my_percent \\% of your sequences are too short"
  msgs_hash['threshold'] = 10
  msgs_hash['warning'] = 'W2'

  plugin_fix_hash['short insert'] = msgs_hash
  msgs_hash = {}

  msgs_hash['msg'] = "Warning!, a my_percent \\% of your sequences are empty (without an insert)"
  msgs_hash['warning'] = 'W3'
  msgs_hash['threshold'] = 1

  plugin_fix_hash['empty insert'] = msgs_hash
  msgs_hash = {}

  msgs_hash['msg'] = "Warning!, a my_percent \\% of your sequences are from a contaminant organism or from organelles"
  msgs_hash['warning'] = 'W4'
  msgs_hash['threshold'] = 1

  plugin_fix_hash['contaminated'] = msgs_hash
  msgs_hash = {}

  msgs_hash['msg'] = "Warning!, a my_percent \\% of your sequences are no valid sequences"
  msgs_hash['threshold'] = 0.1
  msgs_hash['warning'] = 'W5'

  plugin_fix_hash['No valid inserts found'] = msgs_hash
  msgs_hash = {}

  msgs_hash['msg'] = "Warning!, a my_percent \\% of your sequences are low complexity sequences"
  msgs_hash['warning'] = 'W6'
  msgs_hash['threshold'] = 1

  plugin_fix_hash['low complexity by polyt'] = msgs_hash
  msgs_hash = {}

  msgs_hash['msg'] = "Warning!, a my_percent \\% of your sequences contain a vector in an unexpected position"
  msgs_hash['warning'] = 'W7'
  msgs_hash['threshold'] = 1

  plugin_fix_hash['unexpected vector'] = msgs_hash
  msgs_hash = {}

  msgs_hash['msg'] = "Warning!, a my_percent \\% of your sequences contain too much indeterminations"
  msgs_hash['threshold'] = 0.1
  msgs_hash['warning'] = 'W8'

  plugin_fix_hash['Indeterminations in middle of sequence'] = msgs_hash
  msgs_hash = {}

msgs_hash['msg'] = "Warning!, a my_percent \\% of your sequences are too big or too small"
msgs_hash['threshold'] = 1
msgs_hash['warning'] = 'W9'

plugin_fix_hash['size out of limits'] = msgs_hash
msgs_hash = {}

  msgs_hash['msg'] = "WT  Warning!, a my_percent \\% of your sequences were rejected!"
  msgs_hash['threshold'] = 25
  msgs_hash['warning'] = 'WT'

  plugin_fix_hash['rejected'] = msgs_hash
  msgs_hash = {}

  puts JSON.pretty_generate(plugin_fix_hash)

end