Class: SequenceWithAction

Inherits:
Sequence show all
Defined in:
lib/seqtrimnext/classes/sequence_with_action.rb

Overview

Author

Almudena Bocinos Rioboo

This class create the structure to storage the actions associated to a sequence. It allows to add action, and to write at file the actions for every sequence

Inherit

Sequence

Constant Summary collapse

SHOW_QUAL = 
false
SHOW_FINAL_INSERTS = 
true

Instance Attribute Summary collapse

Attributes inherited from Sequence

#seq_comment, #seq_fasta, #seq_name, #seq_qual, #seq_rejected, #seq_rejected_by_message, #seq_repeated, #seq_reversed

Instance Method Summary collapse

Methods inherited from Sequence

#ns_present?, #seq_is_long_enough, #to_fasta, #to_qual, #xs_present?

Constructor Details

#initialize(seq_name, seq_fasta, seq_qual, seq_comment = '') ⇒ SequenceWithAction

Creates an instance with the structure to storage the actions associated to a sequence



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 21

def initialize(seq_name,seq_fasta,seq_qual, seq_comment = '')
  super

  @actions = []
  @seq_fasta_orig = seq_fasta
  @seq_fasta = seq_fasta
  
  @seq_qual_orig = seq_qual
  @seq_qual = seq_qual     
  
  @insert_start = 0
  @insert_end = seq_fasta.length-1 
  
  @stats={}
  @comments=[]
  
  @file_tags=[]
  
  # for paired ends
  @order_in_tuple=0
  @tuple_id=0
  @tuple_size=0
  @file_tag_tuple_priority=0
  
end

Instance Attribute Details

#actions ⇒ Object

Returns the value of attribute actions.



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 18

def actions
  @actions
end

#insert_end ⇒ Object

Returns the value of attribute insert_end.



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 18

def insert_end
  @insert_end
end

#insert_end_last ⇒ Object

Returns the value of attribute insert_end_last.



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 18

def insert_end_last
  @insert_end_last
end

#insert_start ⇒ Object

Returns the value of attribute insert_start.



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 18

def insert_start
  @insert_start
end

#insert_start_last ⇒ Object

Returns the value of attribute insert_start_last.



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 18

def insert_start_last
  @insert_start_last
end

#order_in_tuple ⇒ Object

Returns the value of attribute order_in_tuple.



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 18

def order_in_tuple
  @order_in_tuple
end

#seq_fasta_orig ⇒ Object

Returns the value of attribute seq_fasta_orig.



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 18

def seq_fasta_orig
  @seq_fasta_orig
end

#seq_qual_orig ⇒ Object

Returns the value of attribute seq_qual_orig.



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 18

def seq_qual_orig
  @seq_qual_orig
end

#stats ⇒ Object

Returns the value of attribute stats.



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 18

def stats
  @stats
end

#tuple_id ⇒ Object

Returns the value of attribute tuple_id.



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 18

def tuple_id
  @tuple_id
end

#tuple_size ⇒ Object

Returns the value of attribute tuple_size.



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 18

def tuple_size
  @tuple_size
end

Instance Method Details

#action_right(a, p_beg, p_end) ⇒ Object 



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 431

def action_right(a,p_beg,p_end) 
  
    # $LOG.debug " is right action" if ((a.start_pos-p_beg)>(p_end-a.end_pos-1))   
    # $LOG.debug " is left action " if !((a.start_pos-p_beg)>(p_end-a.end_pos-1))   
    return ((a.start_pos-p_beg)>(p_end-a.end_pos-1))
  
end

#add_action(a) ⇒ Object

Adds a new action to the sequence



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 91

def add_action(a)
  $LOG.debug("Adding action #{a.type} to #{seq_name}")
        
  @actions.push a
  
  a.apply_to(self)
  
  return a
  
end

#add_actions(actions) ⇒ Object

TODO - Nuevo algoritmo de corte de seqs. 1 - Ordenar seqs con cut=true en izq y der y por posición de ends o begs 2 - Obtener izq.ends.max y der.begs.min 3 - El corte lo definen esos min y max



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 128

def add_actions(actions)
             
 if !actions.empty?             
    start_pos=0
    end_pos = 0
    cut = false              

    max_end_pos = 0 
    
        
    
    p_beg = @insert_start
    p_end = @seq_fasta.length-1+@insert_start   
    # p_end = @seq_fasta.length-1   
    # puts "ADDING ACTIONS"
    # puts "=" * 50
    # puts 'actions ' + actions.inspect                               
    # para cada accion ordenada por start_pos
    actions.sort{|e,f| e.start_pos<=>f.start_pos}.each do |action| 
      # puts ' current ' + action.inspect
      # puts " UUUUUUUUUU1 "
      # puts "vect in pos #{action.start_pos} #{action.end_pos}" if (action.type=='ActionVectors') 
      # puts " UUUUUUUUUU2 " 
                     
      # puts "ADD ACTION:",action.to_json
                      
      # añadir el inicio del inserto si es necesario         
      if action.start_pos !=0 or action.end_pos != 0
         action.start_pos+=@insert_start    
         action.end_pos+=@insert_start            
      end       
      
      # guardar accion  
      a = add_action(action)
      
      start_pos= a.start_pos                     
      end_pos=a.end_pos             
                                 
                    
      # si hay que cortar y es accion izquierda
      # if (a.cut && ( left_action(@seq_fasta,start_pos-p_beg,end_pos) ||   # action is left in insert
      if (a.cut && a.left_action?(@seq_fasta.length))
      # if (a.cut && ( a.left_action==true || 
      #                       ( a.right_action==false && (left_action(@seq_fasta,start_pos-p_beg,end_pos-p_beg) ||   # action is left in insert
      #                        (start_pos==p_beg)) )))     # action is right in insert but it's continous to the before action  
      #              
          # puts "in seq w action left act  #{start_pos} #{end_pos} pbeg #{p_beg} p_end #{p_end}"                                                                        
           # puts "Cut left: #{a.inspect}"
          if (end_pos+1) > p_beg
            p_beg=end_pos+1
          end
          a.left_action=true
          cut=true     
          # puts "in seq w action left act  #{start_pos} #{end_pos} pbeg #{p_beg} p_end #{p_end}"                                                                        
          
       # elsif (a.cut && right_action(@seq_fasta,start_pos-p_beg,end_pos)) # action is rigth  in insert
      elsif (a.cut && a.right_action?(@seq_fasta.length))
        # puts "Cut right: #{a.inspect}"
       # elsif (a.cut && (a.right_action==true || right_action(@seq_fasta,start_pos-p_beg,end_pos-p_beg))) # action is rigth  in insert 
          # puts "in seq w action right act  #{start_pos} #{end_pos} pbeg #{p_beg} p_end #{p_end}"   
          if (start_pos-1) < p_end
            p_end = start_pos-1   
          end
          a.right_action=true
          cut=true  
          # puts "in seq w action right act  #{start_pos} #{end_pos} pbeg #{p_beg} p_end #{p_end}"  
      elsif !a.cut
          # puts "NO cut action"
          if a.right_action?(@seq_fasta.length)
            a.right_action=true
          else
            a.left_action = true
          end

      end  
       
      # puts "p_beg: #{p_beg} , p_end: #{p_end}"
     
   end
   
 
   if cut then 
            
     @seq_fasta = @seq_fasta_orig[p_beg..p_end] 
     # puts @seq_fasta
     @seq_qual = @seq_qual_orig[p_beg..p_end] if !@seq_qual_orig.nil?
                 
     # puts "in seq w action1 #{@insert_start} #{@insert_end}"
     @insert_start = p_beg
     size_cut_right = @insert_end - p_end
     @insert_end -= size_cut_right
     # puts "in seq w action2 #{@insert_start} #{@insert_end}" 
     
     
   end    
  end
end

#add_actions_no_left_rigth_parameters(actions) ⇒ Object

Adds a set of actions to the sequence, update the positon of the cut sequence. # Version without the parameters left_action and rigth action #



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 230

def add_actions_no_left_rigth_parameters(actions)
             
 if !actions.empty?
    start_pos=0
    end_pos = 0
    cut = false              

    max_end_pos = 0 
    
        
    
    p_beg = @insert_start
    p_end = @seq_fasta.length-1+@insert_start   
    # p_end = @seq_fasta.length-1   
          
    # puts 'actions ' + actions.inspect                               
    # para cada accion ordenada por start_pos
    actions.sort!{|e,f| e.start_pos<=>f.start_pos}.each do |action| 
      # puts ' current ' + action.inspect
      # puts " UUUUUUUUUU1 "
      # puts "vect in pos #{action.start_pos} #{action.end_pos}" if (action.type=='ActionVectors') 
      # puts " UUUUUUUUUU2 " 
                     
      # puts "ADD ACTION:",action.to_json
                      
      # añadir el inicio del inserto si es necesario         
      if action.start_pos !=0 or action.end_pos != 0
         action.start_pos+=@insert_start    
         action.end_pos+=@insert_start            
      end       
      
      # guardar accion  
      a = add_action(action)
      
      start_pos= a.start_pos                     
      end_pos=a.end_pos             
                                 
                     
      # si hay que cortar y es accion izquierda
      # if (a.cut && ( left_action(@seq_fasta,start_pos-p_beg,end_pos) ||   # action is left in insert
      if (a.cut && ( left_action(@seq_fasta,start_pos-p_beg,end_pos-p_beg) ||   # action is left in insert
                    (start_pos==p_beg)) )     # action is right in insert but it's continous to the before action  
          
          puts "in seq w action left act  #{start_pos} #{end_pos} pbeg #{p_beg} p_end #{p_end}"                                                                        
          
          p_beg=end_pos+1
          cut=true     
          a.left_action=true
          # puts "in seq w action left act  #{start_pos} #{end_pos} pbeg #{p_beg} p_end #{p_end}"                                                                        
          
       # elsif (a.cut && right_action(@seq_fasta,start_pos-p_beg,end_pos)) # action is rigth  in insert 
       elsif (a.cut && right_action(@seq_fasta,start_pos-p_beg,end_pos-p_beg)) # action is rigth  in insert 
          puts "in seq w action right act  #{start_pos} #{end_pos} pbeg #{p_beg} p_end #{p_end}"  
          p_end = start_pos-1   
          a.right_action=true
          cut=true  
          # puts "in seq w action right act  #{start_pos} #{end_pos} pbeg #{p_beg} p_end #{p_end}"  
       elsif !a.cut
         puts "NO cut action"
         if right_action(@seq_fasta,start_pos-p_beg,end_pos-p_beg)
           a.right_action=true
         end
         
       end  
       
 
     
   end
   
 
   if cut then 
            
     @seq_fasta = @seq_fasta_orig[p_beg..p_end] 
     @seq_qual = @seq_qual_orig[p_beg..p_end] if !@seq_qual_orig.nil?
                 
     # puts "in seq w action1 #{@insert_start} #{@insert_end}"
     @insert_start = p_beg
     size_cut_right = @insert_end - p_end
     @insert_end -= size_cut_right   
     # puts "in seq w action2 #{@insert_start} #{@insert_end}" 
     
 
     
   end    
  end
end

#add_comment(comment) ⇒ Object 



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 47

def add_comment(comment)
  @comments.push comment
end

#add_file_tag(tag_level, tag_value, tag_type, priority = 0) ⇒ Object

add a file tag to sequence



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 56

def add_file_tag(tag_level, tag_value, tag_type, priority=0)
  @file_tags<< {:level => tag_level, :name => tag_value, :type=> tag_type}
  @file_tag_tuple_priority=priority
end

#get_actions(type = nil) ⇒ Object

Receive a type of action. Be carefull, type is not a string . Return an array of actions of this type



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 446

def get_actions(type=nil)
   res = []
             
   @actions.each do |a|
      if a.is_a?(type) or type.nil?
        res.push a
      end
   end
   
   return res
end

#get_comment_line ⇒ Object 



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 51

def get_comment_line
  return ([@seq_rejected_by_message]+@comments).compact.join(';')
end

#get_file_tag_path ⇒ Object

join file tags into a path



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 62

def get_file_tag_path
  levels=@file_tags.map{|e| e[:level]}.uniq

  dirpath = []
  levels.sort.each do |level|
    # select names from all that are not files
    level_path = @file_tags.select{|e| ((e[:level]==level) && (e[:type]!=:file))}.map{|tag| tag[:name]}
    dirpath << level_path.join('_') if !level_path.empty?
  end
  
  filepath = []
  levels.sort.each do |level|
    # select names from all that are not files
    level_path = @file_tags.select{|e| ((e[:level]==level) && (e[:type]!=:dir))}.map{|tag| tag[:name]}
    filepath << level_path.join('_') if !level_path.empty?
  end
  
  
  filename=filepath.join('_')
  dirname=File.join(dirpath)
  
  
  # puts "#{dirname}, #{filename}"
  
  return [dirname,filename,@file_tag_tuple_priority]
  
end

#get_inserts ⇒ Object 



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 461

def get_inserts
   
  inserts = get_actions(ActionInsert)
  
  res =[]         
  inserts.each do |insert|
    res.push @seq_fasta_orig[insert.start_pos..insert.end_pos]
  end

  return res 

end

#get_qual_inserts ⇒ Object 



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 474

def get_qual_inserts
   
  inserts = get_actions(ActionInsert)
  
  res =[]
  
  if @seq_qual_orig
    inserts.each do |insert|
      res.push @seq_qual_orig[insert.start_pos..insert.end_pos]
    end
  end
  
  return res 

end

#insert_bounds ⇒ Object 



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 490

def insert_bounds
  return [@insert_start,@insert_end]
end

#new_action(start_pos, end_pos, action_type) ⇒ Object

Adds a new action to the sequence



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 103

def new_action(start_pos,end_pos,action_type)
  
  a = ActionManager.new_action(start_pos,end_pos,action_type)
  
  return a
  
end

#range_inside_action_type?(q_beg, q_end, action_type) ⇒ Boolean

check if range defined by q_beg and q_end is inside some action of the type indicated by action_type

Returns:

  • (Boolean) 


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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 318

def range_inside_action_type?(q_beg,q_end,action_type)
		res = false

action_list = get_actions(action_type)

action_list.each do |action|
	
	if action.contains_action?(q_beg+@insert_start,q_end+@insert_start,10)
		res = true
		break
	end
end
		
		return res

end

#save_to_file ⇒ Object

Saves a sequence with its actions to a file



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 418

def save_to_file
  File.open("results/#{seq_name}"+".txt", 'w') { |file|
   
    n=1
    
    @actions.each do |a|
      file.puts a.description
      n +=1   
    end
  } 
  
end

#to_json ⇒ Object 



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 494

def to_json
   s={}
   s[:seq_name]=@seq_name
   s[:seq_fasta]=@seq_fasta_orig
   s[:seq_qual]=''
   if @seq_qual_orig
     s[:seq_qual]=@seq_qual_orig.join(' ')
   end
   s[:rejected]=@rejected
   

   s[:fasta_inserts]= get_inserts
   s[:qual_inserts]=get_qual_inserts.map { |e| e.join(' ') }
   s[:actions]=[]
   
   @actions.each { |a| s[:actions].push a.to_hash }
   # puts "YAML",s.to_yaml
   return JSON.pretty_generate(s)
end

#to_text ⇒ Object

Prints a sequence with its actions to a file



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 338

def to_text
  
    output_res=[]
    
    if @seq_rejected
      output_res<< "[#{@tuple_id},#{@order_in_tuple}] Sequence #{seq_name} had the next actions: ".bold.underline + " REJECTED:  #{@seq_rejected_by_message}".red    
      # puts  @seq_name.bold + bold + ' REJECTED BECAUSE ' +@seq_rejected_by_message.bold if @seq_rejected 
    else
      output_res<< "[#{@tuple_id},#{@order_in_tuple}] Sequence #{seq_name} had the next actions: ".bold.underline  
      
    end
    
    n=1
    withMessage = ["ActionIsContaminated","ActionVectors","ActionBadAdapter","ActionLeftAdapter","ActionRightAdapter"]  
    color = red
    
    @actions.sort!{|e,f| e.start_pos<=>f.start_pos}.each do |a|     
      a_type=a.action_type
      color = a.apply_decoration(" EXAMPLE ") 
      color2 =a.apply_decoration(" #{a_type.center(8)} ") 
         
      reversed_str = ''    
      
      if a.reversed
        reversed_str = "   REVERSED  ".bold 
      end
      
      output_res<< " [#{n}] ".bold + color2+ " #{a.title} ".ljust(24).reset  +  " [ " + " #{a.start_pos+1}".center(6) + " , " + "#{a.end_pos+1}".center(6) + " ]" +  clear.to_s + "#{a.message}".rjust(a.message.size+8) + reversed_str
      
      n +=1   
    end
    
    pos = 0
    res = '' 
    
    @seq_fasta_orig.each_char do |c|
      
      @actions.each do |a|
        c= a.decorate(c,pos) 
        
      end 
      
      res += c
      
      pos += 1
    end       
            
    output_res<< res
    
    if SHOW_QUAL and @seq_qual_orig
       res = '' 
       pos=0               
       output_res<< ''
      @seq_fasta_orig.each_char do |c2|
        c=@seq_qual_orig[pos].to_s+' '
        @actions.each do |a|
          c= a.decorate(c,pos) 

        end 
        res += c
        pos += 1
      end
             
      output_res<< res
    end
    
    if SHOW_FINAL_INSERTS      		 
       output_res<<  "INSERT ==>"+get_inserts.join("\nINSERT ==>")
       output_res<< "="*80
    end
    # puts  @seq_name.bold + bold + ' rejected because ' +@seq_rejected_by_message.bold if @seq_rejected                 

    return output_res
end

#to_text_seq_fasta ⇒ Object 



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# File 'lib/seqtrimnext/classes/sequence_with_action.rb', line 413

def to_text_seq_fasta
   return " "*@insert_start +@seq_fasta
end