Class: UneLosHit

Inherits:
Object
  • Object
show all
Defined in:
lib/full_lengther_next/classes/une_los_hit.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(q, query_fasta, pident_threshold) ⇒ UneLosHit

Returns a new instance of UneLosHit.



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# File 'lib/full_lengther_next/classes/une_los_hit.rb', line 9

def initialize(q, query_fasta, pident_threshold)
			
	(mismas_ids_array, query_fasta, wrong_seq) = hits_misma_id(q, query_fasta)
	
	@wrong_seq = wrong_seq
	@mismas_ids_array = mismas_ids_array
	@msgs = ''
	@number_x = 0
	num_x = ''
	
	@output_seq = query_fasta
	
	if (mismas_ids_array.count > 1)
		mismas_ids_array.sort! {|h1,h2| h1.q_beg <=> h2.q_beg} # ordenamos los hit por el inicio del query
		@final_hit = mismas_ids_array[0].dup

		mismas_ids_array.each do |hit|
			if (hit.ident >= pident_threshold)
				# if ($verbose)
					# puts "#{hit.acc}\tsc:#{hit.score}\teval:#{hit.e_val}\tid:#{hit.ident}\tframe:#{hit.q_frame}\tqb:#{hit.q_beg + 1}\tqe:#{hit.q_end + 1}\tsb:#{hit.s_beg + 1}\tse:#{hit.s_end + 1}"
					# puts "#{query_fasta[hit.q_beg..hit.q_end].translate}"
				# end
			
				same = same_hit(hit)
		
				if (!same)
					if (@final_hit.q_frame == hit.q_frame)
						same_frame_hits(hit)
					else
						# condiciones para corregir el frame en el que tiene que continuar la seq de nt
						correccion_x = 0
						if (@final_hit.q_frame - hit.q_frame == 1)
							correccion_x = 1
						elsif (@final_hit.q_frame - hit.q_frame == 2)
							correccion_x = 2
						elsif (@final_hit.q_frame - hit.q_frame == -1)
							correccion_x = 2
						elsif (@final_hit.q_frame - hit.q_frame == -2)
							correccion_x = 1
						end
					
						# las secuencias solapan en el query
						if ((@final_hit.q_end >= hit.q_beg) && (@final_hit.q_end < hit.q_end)) && (hit.q_end > @final_hit.q_end + 15)
							overlapped_hits(hit, correccion_x, q)
							# puts "---#{@output_seq[@final_hit.q_frame-1, @output_seq.length+1].translate}"
					
						elsif (@final_hit.q_end < hit.q_beg) && (hit.q_end > @final_hit.q_end + 15) # las secuencias estan separadas en el query
							separated_hits(hit, correccion_x, q)
							# puts "----------#{@output_seq[@final_hit.q_frame-1, @output_seq.length+1].translate}"
						else
							@msgs = 'warning!, putative chimeric sequence! or repetitive structure'
							# puts "\nWARNING!, PUTATIVE CHIMERIC SEQUENCE !!!\n\n"
						end
					end
				end
			end # pident
		end

	else

		@final_hit = mismas_ids_array[0].dup
		
		# if ($verbose)
			# puts "***#{@final_hit.acc}\t#{@final_hit.score}\t#{@final_hit.e_val}\t#{@final_hit.ident}\t#{@final_hit.align_len}\t#{@final_hit.q_frame}\t#{@final_hit.q_beg + 1}\t#{@final_hit.q_end + 1}\t#{@final_hit.s_beg + 1}\t#{@final_hit.s_end + 1}\t#{@final_hit.q_seq}"
			# puts "#{query_fasta[@final_hit.q_beg..@final_hit.q_end].translate}"
		# end
	end
	# puts "***#{@final_hit.acc}\t#{@final_hit.score}\t#{@final_hit.e_val}\t#{@final_hit.ident}\t#{@final_hit.align_len}\t#{@final_hit.q_frame}\t#{@final_hit.q_beg + 1}\t#{@final_hit.q_end + 1}\t#{@final_hit.s_beg + 1}\t#{@final_hit.s_end + 1}\t#{@final_hit.q_seq}"
	# puts "#{query_fasta[@final_hit.q_beg..@final_hit.q_end].translate}"
	
	@full_prot = @output_seq[@final_hit.q_frame-1, @output_seq.length+1].translate
	# puts "\nfull_prot_ulh: \n#{full_prot}"
	
	(@is_ok, @q_index_start) = contenidos_en_prot(@final_hit, @full_prot, q)
	
end

Instance Attribute Details

#final_hit ⇒ Object (readonly)

Returns the value of attribute final_hit.



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# File 'lib/full_lengther_next/classes/une_los_hit.rb', line 7

def final_hit
  @final_hit
end

#full_prot ⇒ Object (readonly)

Returns the value of attribute full_prot.



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# File 'lib/full_lengther_next/classes/une_los_hit.rb', line 7

def full_prot
  @full_prot
end

#is_ok ⇒ Object (readonly)

Returns the value of attribute is_ok.



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# File 'lib/full_lengther_next/classes/une_los_hit.rb', line 7

def is_ok
  @is_ok
end

#msgs ⇒ Object (readonly)

Returns the value of attribute msgs.



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# File 'lib/full_lengther_next/classes/une_los_hit.rb', line 7

def msgs
  @msgs
end

#number_x ⇒ Object (readonly)

Returns the value of attribute number_x.



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# File 'lib/full_lengther_next/classes/une_los_hit.rb', line 7

def number_x
  @number_x
end

#output_seq ⇒ Object (readonly)

Returns the value of attribute output_seq.



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# File 'lib/full_lengther_next/classes/une_los_hit.rb', line 7

def output_seq
  @output_seq
end

#q_index_start ⇒ Object (readonly)

Returns the value of attribute q_index_start.



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# File 'lib/full_lengther_next/classes/une_los_hit.rb', line 7

def q_index_start
  @q_index_start
end

#wrong_seq ⇒ Object (readonly)

Returns the value of attribute wrong_seq.



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# File 'lib/full_lengther_next/classes/une_los_hit.rb', line 7

def wrong_seq
  @wrong_seq
end

Instance Method Details

#hits_misma_id(q, query_fasta_ori) ⇒ Object

creamos un array en el que esten solo los hits con la misma id.



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# File 'lib/full_lengther_next/classes/une_los_hit.rb', line 248

def hits_misma_id(q, query_fasta_ori)
	
	# Se les hace la reveso complementaria si es necesario, y se comprueba que para un mismo query no hay hits en sentidos diferentes
	wrong_seq = false
	
	misma_id = []
	
	query_fasta = query_fasta_ori.dup
	frame_ori = q.hits[0].q_frame

	q.hits.each do |h|

		# puts "#{q.query_def} f_ori :#{frame_ori} y h_f: #{h.q_frame}"
		reversed_hit = false # con respecto al primer hit, que es el de mayor score o evalue
		if (h.acc == q.hits[0].acc)

			# comprobar si los frames tiene el mismo sentido
			if ((frame_ori < 0 && h.q_frame > 0) or (frame_ori > 0 && h.q_frame < 0))
				wrong_seq = true
				reversed_hit = true
				# puts "The sequence #{q.query_def} contains sense and antisense hits!!! #{frame_ori} y #{h.q_frame}"
			end
			
			if (reversed_hit == false)
				if (h.q_frame.to_i < 0) # si la secuencia esta al reves le damos la vuelta
					(query_fasta, h.q_frame, h.q_beg, h.q_end) = reverse_seq(query_fasta_ori, h.q_frame, h.q_beg, h.q_end)
					h.reversed = true
				end
				misma_id.push h
			end

		end

	end

	return [misma_id, query_fasta, wrong_seq]
end

#overlapped_hits(hit, correccion_x, q) ⇒ Object 



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# File 'lib/full_lengther_next/classes/une_los_hit.rb', line 117

def overlapped_hits(hit,correccion_x,q)
  # puts q.inspect
	# puts "los hits solapan!!!"
	
	if (@msgs.empty?)
		@msgs = "Overlapping hits, possible frame ERROR between #{@final_hit.q_end + 1} and #{hit.q_beg + 1}, "
	else
		@msgs += " and overlapping frame ERROR between #{@final_hit.q_end + 1} and #{hit.q_beg + 1}, "
	end
	
	# -------------------------------------   preparamos los nt y aas que solapan
	overlapped_nt = 0
	overlapped_nt = (@final_hit.q_end - hit.q_beg + 1)

	overlapped_aas = 0
	overlapped_aas = (@final_hit.s_end - hit.s_beg + 1)
	# ------------------------------------- 
	if (overlapped_nt % 3 == 1)
		overlapped_nt += 2
	elsif (overlapped_nt % 3 == 2)
		overlapped_nt += 1
	end
	# -------------------------------------   calculamos el numero de x a añadir 
	@number_x = (((correccion_x + overlapped_nt)/3)+1)*3
	@number_x_aa = overlapped_aas
	num_x = ''
	num_x_aa = ''

	if (@number_x.to_i > 0)
		num_x = 'x'*@number_x.to_i
	elsif (@number_x.to_i == 0)
		num_x = ''
	else
		@msgs = "ERROR#2 unexpected negative index in x_number, "
		# puts "ERROR#2 unexpected negative index in x_number"
	end

	if (@number_x_aa.to_i > 0)
		num_x_aa = 'x'*@number_x_aa.to_i
	elsif (@number_x_aa.to_i == 0)
		num_x_aa = ''
	else
		num_x_aa = 'x'*@number_x_aa.to_i.abs
		@msgs = "Warning!, your query overlaps and the subject is separated, "
	end

	if (@number_x_aa.to_i >= 0)
		@final_hit.q_seq = "#{@final_hit.q_seq[0..@final_hit.q_seq.length - 1 - overlapped_aas]}#{num_x_aa}#{hit.q_seq[overlapped_aas..hit.q_seq.length]}"
		@final_hit.s_seq = "#{@final_hit.s_seq[0..@final_hit.s_seq.length - 1 - overlapped_aas]}#{num_x_aa}#{hit.s_seq[overlapped_aas..hit.s_seq.length]}"
	else
		@final_hit.q_seq = "#{@final_hit.q_seq[0..@final_hit.q_seq.length - 1]}#{num_x_aa}#{hit.q_seq[0..hit.q_seq.length]}"
		@final_hit.s_seq = "#{@final_hit.s_seq[0..@final_hit.s_seq.length - 1]}#{num_x_aa}#{hit.s_seq[0..hit.s_seq.length]}"
	end
	
	
	output_seq_tmp = "#{@output_seq[0..(@final_hit.q_end - overlapped_nt)]}#{num_x}#{@output_seq[(hit.q_beg + overlapped_nt)..(@output_seq.length)]}"

	full_prot_tmp = output_seq_tmp[@final_hit.q_frame-1, output_seq_tmp.length+1].translate
	
	(is_ok_tmp, q_index_start_tmp) = contenidos_en_prot(@final_hit, full_prot_tmp, q)

	@output_seq = output_seq_tmp.dup
	
	@final_hit.q_beg = @final_hit.q_beg
	@final_hit.q_end = hit.q_end
	
	@final_hit.s_beg = [@final_hit.s_beg,hit.s_beg].min
	@final_hit.s_end = [@final_hit.s_end,hit.s_end].max
	
end

#same_frame_hits(hit) ⇒ Object 



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# File 'lib/full_lengther_next/classes/une_los_hit.rb', line 105

def same_frame_hits(hit)
	
	@final_hit.q_beg = @final_hit.q_beg
	@final_hit.q_end = hit.q_end
	
	@final_hit.s_beg = [@final_hit.s_beg,hit.s_beg].min
	@final_hit.s_end = [@final_hit.s_end,hit.s_end].max
	
end

#same_hit(hit) ⇒ Object 



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# File 'lib/full_lengther_next/classes/une_los_hit.rb', line 88

def same_hit(hit)

	same = false
	if (hit.score == @final_hit.score &&
		hit.q_beg == @final_hit.q_beg &&
		hit.q_end == @final_hit.q_end &&
		hit.s_beg == @final_hit.s_beg &&
		hit.s_end == @final_hit.s_end)
	
		same = true
	end

	return same
end

#separated_hits(hit, correccion_x, q) ⇒ Object 



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# File 'lib/full_lengther_next/classes/une_los_hit.rb', line 190

def separated_hits(hit,correccion_x,q)
	
	# puts "los hits estan separados!!!"
	
	if (@msgs.empty?)
		@msgs = "Separated hits, possible frame ERROR between #{@final_hit.q_end + 1} and #{hit.q_beg + 1}, "
	else
		@msgs += " and possible frame ERROR between #{@final_hit.q_end + 1} and #{hit.q_beg + 1}, "
	end
	
	# PROBAR CON % 3!!!!!!!!!!!!!!!!!!!!!!!!
	@number_x = (hit.q_beg - @final_hit.q_end - 1)
	# @number_x = (hit.q_beg - @final_hit.q_end - 1) + correccion_x
	if (@number_x % 3 == 1)
		@number_x += 2
	elsif (@number_x % 3 == 2)
		@number_x += 1
	end
	

	if (@number_x.to_i > 0)
		num_x = 'x'*@number_x.to_i
		num_x_aa = 'x'*(@number_x.to_i/3)
	elsif (@number_x.to_i == 0)
		num_x = ''
		num_x_aa = ''
	else
		@msgs = "ERROR#2 unexpected negative index in x_number"
		# puts "ERROR#2 unexpected negative index in x_number"
	end

	@output_seq = @output_seq[0..@final_hit.q_end-1]+num_x+@output_seq[hit.q_beg-1..@output_seq.length-1]
	# @output_seq = @output_seq[0..@final_hit.q_end-1]+num_x+@output_seq[hit.q_beg-1..@output_seq.length-1]

	@final_hit.score += 1
	@final_hit.q_beg = @final_hit.q_beg
	@final_hit.q_end = hit.q_end
	@final_hit.s_beg = @final_hit.s_beg
	@final_hit.s_end = hit.s_end

	@final_hit.q_seq = "#{@final_hit.q_seq[0, @final_hit.q_seq.length]}#{num_x_aa}#{hit.q_seq[0, hit.q_seq.length]}"
	@final_hit.s_seq = "#{@final_hit.s_seq[0, @final_hit.s_seq.length]}#{num_x_aa}#{hit.s_seq[0, hit.s_seq.length]}"

	num_x = ''
	num_x_aa = ''
	
	full_prot_tmp = @output_seq[@final_hit.q_frame-1, @output_seq.length+1].translate
	# puts "\n\nfull_prot_tmp:#{full_prot_tmp}"
	# puts "\n\n#{@output_seq[@final_hit.q_frame-1, @output_seq.length+1]}"
	
	(is_ok_tmp, q_index_start_tmp) = contenidos_en_prot(@final_hit, full_prot_tmp, q)
	
	# puts "#{q.query_def}: is_ok_tmp: #{is_ok_tmp} separated hits"
end