Class: TestCode

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

Instance Method Summary collapse

Constructor Details

#initialize(seq) ⇒ TestCode

Returns a new instance of TestCode.



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# File 'lib/full_lengther_next/test_code.rb', line 9

def initialize(seq)
	
	name=''
	t_code=''
	status=''
	ref_start=0
	ref_end=seq.seq_fasta.length
	ref_frame=''
	orf=''
	protein = ''
	p_long = 0
	
	if seq.fasta_length < 200			
		seq.type = UNKNOWN
		seq.test_code(0.0)
		seq.warnings('<200nt')
		seq.hit = [ref_start, ref_end, 0] #Last element is ref_frame
	else
		
# para probar tescode con toda la secuencia, en lugar de con los ORFs ----------------------------------------------------------------------
		# sense_strand = seq.seq_fasta.upcase
		# antisense_strand = sense_strand.complementary_dna
		# (t_code,t_status) = testCode_exec(sense_strand)
		# ref_frame = 1
		# ref_msgs = ''
		# (as_t_code,as_t_status) = testCode_exec(antisense_strand)
		# # puts "#{seq.seq_name}: t_code: #{t_code}, t_status: #{t_status}, as_t_code: #{as_t_code}, as_t_status: #{as_t_status}"
		# seq.annotate(:tcode,"#{seq.seq_name}\t#{seq.seq_fasta.length}\t\ttestcode\t#{t_status}\t#{t_code}\t\t\t\t\t#{ref_msgs}\t#{ref_frame}\t#{ref_start}\t#{ref_end}\t\t\t\t",true)
# --------------------------------------------------------------------------------------------------------------------------------


		# see add_region filter
		name,t_code,status,ref_start,ref_end,ref_frame,orf,ref_msgs,stop_before_start,more_than_one_frame = t_code(seq)
		seq.test_code(t_code)
		seq.warnings(ref_msgs)
		seq.hit = [ref_start, ref_end, ref_frame]

		if status == :unknown
			seq.type = UNKNOWN
		else
			seq.type = CODING
		end
		
		# if (ref_msgs.nil?)
		# 	ref_msgs = ''
		# end
		# 
		# if (stop_before_start)
		# 	ref_msgs += "There is a STOP codon before ATG. "
		# end
		# 
		# if (more_than_one_frame)
		# 	ref_msgs += "Possible frame error by an ins/del"
		# end
		# 
		# if (status.to_s =~ /^[CN]\_terminus/) || (status == :Internal)
		# 	tmp_status = "Putative #{status.to_s}"
		# else
		# 	tmp_status = status.to_s
		# end
		# 
		# 	
		# if (!orf.nil?) && (!more_than_one_frame)
		# 	protein = orf.translate
		# 	p_long = protein.length - 3
		# 	seq.annotate(:tcode,"#{name}\t#{seq.seq_fasta.length}\t\ttestcode\t#{tmp_status}\t#{t_code}\t\t\t#{p_long}\t\t#{ref_msgs}\t#{ref_frame}\t#{ref_start}\t#{ref_end}\t\t\t\t#{protein}",true)
		# else
		# 	seq.annotate(:tcode,"#{name}\t#{seq.seq_fasta.length}\t\ttestcode\t#{tmp_status}\t#{t_code}\t\t\t\t\t#{ref_msgs}\t#{ref_frame}\t#{ref_start}\t#{ref_end}\t\t\t\t",true)
		# end
		
	end
end

Instance Method Details

#add_region(orf_seq, orf_t_start, orf_t_end, orf_frame, orf_stop_codon, orf_type, seq) ⇒ Object

to add regions over a determinated size



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# File 'lib/full_lengther_next/test_code.rb', line 220

def add_region(orf_seq, orf_t_start, orf_t_end, orf_frame, orf_stop_codon, orf_type,seq)

	if (orf_seq.length >= 200)
		# puts "#{seq.seq_name}, #{orf_t_start} - #{orf_t_end}, #{orf_frame}, #{orf_type}"
		seq.add_orf(orf_seq, orf_t_start, orf_t_end, orf_frame, orf_stop_codon, orf_type)
	end

end

#calcParam(valueOne, valueTwo, valueThree) ⇒ Object 



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# File 'lib/full_lengther_next/test_code.rb', line 777

def calcParam (valueOne,valueTwo,valueThree)
	paramArray = [valueOne,valueTwo,valueThree];
	paramArray = paramArray.sort#{|a,b| return a-b}#(compareNumbers);				
	paramValue = paramArray[2] / (paramArray[0] + 1.0);
	# puts paramArray.to_json
	return paramValue;
end

#compare_regions(this_strand, tc_fasta) ⇒ Object

para escoger la region codificante mas grande, incluso solapando verios frames



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# File 'lib/full_lengther_next/test_code.rb', line 205

def compare_regions(this_strand,tc_fasta)
	
	# select the largest ORF without frame repair-------------------------------- hay que comentar todo el bloque de arriba
	best_orf = nil
	best_orf = this_strand.sort{|x,y| y.seq.length <=> x.seq.length }[0]
	
	if !best_orf.nil?
		best_orf.type = best_orf.status
	end
	
	return best_orf

end

#compare_regions_old(this_strand, tc_fasta) ⇒ Object

no se usa para escoger la region codificante mas grande, incluso solapando verios frames



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# File 'lib/full_lengther_next/test_code.rb', line 626

def compare_regions_old(this_strand,tc_fasta)

	# array_regions = []
	# array_regions.push this_strand.first.dup
	# 
	# this_strand.each do |one_orf|
	# 
	# 	prev_orf = array_regions.last.dup # taking last orf before add actual orf
	# 	array_regions.push one_orf.dup # add actual orf, el primer orf me va a salir duplicado
	# 
	# 	if prev_orf.overlaps?(one_orf)
	# 		prev_orf.seq = tc_fasta[prev_orf.t_start..one_orf.t_end]
	# 
	# 		(t_code,t_status)=testCode_exec(prev_orf.seq)
	# 
	# 		prev_orf.score = t_code
	# 		prev_orf.status = t_status
	# 
	# 		#t_start, frame and stop_codon are the same
	# 		prev_orf.t_end = one_orf.t_end
	# 		if (prev_orf.type != one_orf.type)
	# 			prev_orf.type = type_fusion(prev_orf.type,one_orf.type)
	# 		end
	# 		prev_orf.more_than_one_frame = true
	# 
	# 		# puts "overlaps:"
	# 		# puts "#{one_orf.t_start} - #{one_orf.t_end}"
	# 		# puts "#{array_regions.last.t_start} - #{array_regions.last.t_end}"
	# 
	# 		array_regions.push prev_orf # add overlapped orf,
	# 	end
	# 
	# end
	# 
	# # select the largest ORF without frame repair-------------------------------- hay que comentar todo el bloque de arriba
	# # best_orf = nil
	# # best_orf = this_strand.sort{|x,y| y.seq.length <=> x.seq.length }[0]
	# # ---------------------------------------------------------------------------
	# 
	# # select the largest ORF ----------------------------------------------------
	# # best_orf = nil
	# # best_orf = array_regions.sort{|x,y| y.seq.length <=> x.seq.length }[0]
	# # if !best_orf.nil?
	# # 	puts "best_orf.status: #{best_orf.status}, best_orf.type: #{best_orf.type}"
	# # end
	# 
	# 
	# # ---------------------------------------------------------------------------
	# 
	# # select the largest coding ORF ---------------------------------------------
	# best_orf = nil
	# array_regions.sort{|x,y| y.seq.length <=> x.seq.length }.each do |one_orf|
	# 	# puts "#{one_orf.status}, #{one_orf.type}"
	# 	if (one_orf.status == :coding)
	# 		best_orf = one_orf
	# 		break
	# 	end
	# end
	# # ---------------------------------------------------------------------------
	# 
	# # puts "\n\n\nstart"
	# # array_regions.sort{|x,y| y.seq.length <=> x.seq.length }.each do |one_orf|
	# # 	puts one_orf.seq.length
	# # end
	# # puts "end\n\n\n"
	# # puts "best_orf: #{best_orf.seq.length}"
	# 
	# # if !best_orf.nil?
	# # 	best_orf.type = best_orf.status
	# # end
	# 
	# return best_orf

end

#countBases(valueOne, valueTwo, valueThree) ⇒ Object 



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# File 'lib/full_lengther_next/test_code.rb', line 785

def countBases (valueOne,valueTwo,valueThree)
	return valueOne + valueTwo + valueThree;
end

#generate_uncomplete_orf(a, frame, seq) ⇒ Object

se buscan las regiones Complete, N-terminus, C-terminus e Internal en la secuencia de cada frame



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# File 'lib/full_lengther_next/test_code.rb', line 230

def generate_uncomplete_orf(a,frame,seq)
	
	my_atg = true
	atg_codon = false
	stop_codon = false
	any_stop = false
	
	orf =''
	t_start = 0
	t_end = 0
	
	a.each do |e|
		t_end += 3
		orf += e
		
		if (e == 'ATG') && (!atg_codon)
			atg_codon = true
			stop_codon = false
			t_start = t_end - 3
		elsif (e == 'TAG') || (e == 'TGA') || (e == 'TAA')
			orf_tmp = orf[t_start..t_end]
			if (any_stop)
				# case 1, complete orf
				if (atg_codon)
					orf_tmp = orf[t_start..t_end]
					add_region(orf_tmp, t_start, t_end, frame, any_stop, :Complete,seq)
				end
			else
				# case 2, C_terminus
				if (my_atg)
					orf_tmp = orf[0..t_end]
					add_region(orf_tmp, 0, t_end, frame, any_stop, :C_terminus,seq)
					# case 3, putative complete, complete without stop codon before atg
					if (atg_codon)
						orf_tmp = orf[t_start..t_end]
						add_region(orf_tmp, t_start, t_end, frame, any_stop, :Complete, seq)
					end
				end
			end
			
			stop_codon = true
			any_stop = true
			my_atg = false
			atg_codon = false
			t_start += 3
		end
	end
	
	# case 4, N_terminus and case 6, putative N_terminus
	if (atg_codon) && (!stop_codon)
		orf_tmp = orf[t_start..t_end]
		add_region(orf_tmp, t_start, t_end, frame, any_stop, :N_terminus,seq)
	end
	
	# case 5, internal
	if (my_atg) && (!any_stop)
		orf_tmp = orf[0..t_end]
		add_region(orf_tmp, 0, t_end, frame, any_stop, :Internal,seq)
	end
	
end

#getConclusion(testCode_value) ⇒ Object 



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# File 'lib/full_lengther_next/test_code.rb', line 866

def getConclusion (testCode_value)
	codeProb = "";
	if (testCode_value < 0.74)
		codeProb = :unknown;
	elsif (testCode_value >=0.74 and testCode_value < 0.95)
		codeProb = :putative_coding;
	elsif (testCode_value >=0.95)
		codeProb = :coding;
	end

	return codeProb;
end

#orf_fusion(orfs_array, tc_fasta, name, ref_status, ref_code, ref_start, ref_end, ref_frame, ref_orf, ref_msgs) ⇒ Object

no se usa



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# File 'lib/full_lengther_next/test_code.rb', line 349

def orf_fusion(orfs_array,tc_fasta,name,ref_status,ref_code,ref_start,ref_end,ref_frame,ref_orf,ref_msgs)

	lower_start = 9999
	higher_end = 0
	new_orf = false
	ref_name = name

	# vamos a coger el mejor de referencia (el coding mas largo) 
	# y vamos a poner en el warning los coding que estan en el mismo sentido y no estan contenidos en el mejor
	orfs_array.sort! {|orf1,orf2| orf1[1] <=> orf2[1]}

	tmp_orf = ref_orf
	tmp_start = ref_start
	tmp_end = ref_end
	tmp_frame = ref_frame
	tmp_msg = ''

	# puts "\n\n#{name} ---- tmp_frame: #{tmp_frame} ------------------------ \n\n"

	orfs_array.each do |orf|

		(orf[1],orf[2]) = corrige_frame(orf[3],orf[1],orf[2])
		# (orf[1],orf[2]) = $an.corrige_frame(orf[3],orf[1],orf[2])

		# puts "*** name: #{name}, orf[1]: #{orf[1]}, orf[2]: #{orf[2]}, orf[3]: #{orf[3]} ref_start: #{ref_start}, ref_end: #{ref_end}, ref_frame: #{ref_frame} ***\n\n"

		if (orf[0] != tmp_orf)

			if ((tmp_end >= orf[1]) && (tmp_end <= orf[2])) || ((tmp_start >= orf[1]) && (tmp_start <= orf[2])) # los ORFs solapan

				# puts "SOLAPAN     frame: #{orf[3]}  tmp_start: #{tmp_start} tmp_end: #{tmp_end} orf_start: #{orf[1]} orf_end: #{orf[2]}"
				if (tmp_frame > 0)
					tmp_msg = ", overlapping coding region (#{orf[1]},#{orf[2]})"
				elsif (tmp_frame < 0)
					tmp_msg = ", overlapping coding region (-#{orf[1]},-#{orf[2]})"
				end
				new_orf = true

			elsif (tmp_end < orf[1]) || (tmp_start > orf[2]) # los ORFs estan separados

				# puts "#{name}  frame: #{orf[3]}    SEPARADOS --> tmp_start: #{tmp_start} tmp_end: #{tmp_end} orf_start: #{orf[1]} orf_end: #{orf[2]}"
				if (tmp_frame > 0)
					tmp_msg = ", other coding region (#{orf[1]},#{orf[2]})"
				elsif (tmp_frame < 0)
					tmp_msg = ", other coding region (-#{orf[1]},-#{orf[2]})"
				end
				new_orf = true

			end

			if (new_orf == true)

				if (orf[1] < lower_start)
					lower_start = orf[1]
				end

				# if (orf[2] > higher_end)
				# end

				(tmp_code,tmp_status)=testCode_exec(tc_fasta[lower_start-1..higher_end-1])

				if (tmp_status != 'unknown')
					# puts "#{name} ----------------------------------- FUSION!!!!!!!!!!!!!!!!\n\n"
					# tenemos varios ORFs q son codificantes al unirlos
					ref_msgs += tmp_msg
					new_orf = false
				else
					# puts "#{name} ------------------------------------NO se unen\n\n"
				end
			end
		end
	end
	return[ref_status,ref_code,ref_name,ref_start,ref_end,ref_frame,ref_orf,ref_msgs]
end

#t_code(seq) ⇒ Object 



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# File 'lib/full_lengther_next/test_code.rb', line 82

def t_code(seq)
	
	name = seq.seq_name
	tc_fasta = seq.seq_fasta
	
	# generamos todos los ORFs de cada secuencia
	uncomplete_orf_finder(seq)
	minus_strand = []
	plus_strand = []
	
	# puts "**************************************************"
	# puts "#{name} #{tc_fasta.length}"
	# ordenamos los ORFs empezando desde 5' a 3' y luego separamos los de cada hebra en un array distinto
	seq.orfs.sort{|x,y| x.t_start <=> y.t_start }.each do |one_orf|
		
		(t_code,t_status)=testCode_exec(one_orf.seq)
		one_orf.status = t_status
		one_orf.score = t_code
		
		if (one_orf.frame < 0)
			minus_strand.push one_orf
		elsif (one_orf.frame > 0)
			plus_strand.push one_orf
		end
		
	end
	#----------------------------------- Plus strand
	if (!plus_strand.empty?)
		# puts "--------------Plus strand:"
		best_plus_region = compare_regions(plus_strand,tc_fasta)
		if (!best_plus_region.nil?)
			# puts "#{best_plus_region.seq.length}, #{best_plus_region.status}, #{best_plus_region.type}, #{best_plus_region.t_start} - #{best_plus_region.t_end}, #{best_plus_region.frame}"
			# puts best_plus_region.seq
		end
	end
	#----------------------------------- Minus strand
	if (!minus_strand.empty?)
		# puts "--------------Minus strand:"
		best_minus_region = compare_regions(minus_strand,tc_fasta)
		if (!best_minus_region.nil?)
			# puts "#{best_minus_region.seq.length}, #{best_minus_region.status}, #{best_minus_region.type}, #{best_minus_region.t_start} - #{best_minus_region.t_end}, #{best_minus_region.frame}"
			# puts best_minus_region.seq
		end
	end
	# obtenemos la region codificante mas larga de ambas hebras
	best_region = nil
	if (!best_plus_region.nil?)
		if (!best_minus_region.nil?)
			if (best_minus_region.seq.length > best_plus_region.seq.length)
				best_region = best_minus_region
			else
				best_region = best_plus_region
			end
		else
			best_region = best_plus_region
		end
	elsif (!best_minus_region.nil?)
		best_region = best_minus_region
	end
	# puts "--------------Best region:"
	# puts " --------------------------------- #{best_region.seq.length}, #{best_region.status}, #{best_region.type}, #{best_region.t_start} - #{best_region.t_end}, #{best_region.frame}"
	# comprobamos el tipo de ORF segun si tiene un codon de parada antes del atg

	if (!best_region.nil?) && (best_region.seq.length >= 200)
		if (best_region.type == :Complete) && (!best_region.stop_codon)
			best_region.type = 'Putative Complete'
			ref_msgs = 'NO STOP codon before ATG. '
		elsif (best_region.type == :N_terminus) && (!best_region.stop_codon)
			ref_msgs = 'NO STOP codon before ATG. '
		end
		return [name, best_region.score, best_region.type, best_region.t_start, best_region.t_end, best_region.frame, best_region.seq, ref_msgs, best_region.stop_codon, best_region.more_than_one_frame]
	else
		ref_score = 0.0
		ref_start = 0
		ref_end = 0
		ref_frame = 0
		ref_orf = ''
		ref_type = :unknown
		ref_msgs = 'Non coding ORF found >= 200 nt '
		return [name, ref_score, ref_type, ref_start, ref_end, ref_frame, ref_orf, ref_msgs, false, false]
	end
end

#t_code_old(seq) ⇒ Object

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# File 'lib/full_lengther_next/test_code.rb', line 424

def t_code_old(seq)

	ref_code = 0.0
	ref_name = ''
	ref_start = 0
	ref_end = 0
	ref_frame = 0
	ref_status = ''
	ref_orf = ''
	ref_msgs = ''

	name = seq.seq_name
	tc_fasta = seq.seq_fasta
	
	# generamos todos los ORFs mayores de 200pb de cada secuencia, en fl_string_utils
	orfs_array = tc_fasta.orf_finder
	
	if (orfs_array[0].nil?)
		ref_name = name
		ref_code = 0.0
		ref_start = 0
		ref_end = 0
		ref_frame = 0
		ref_status = 'unknown'
		ref_orf = ''
		ref_msgs = 'ORF length < 200 nt'
		# ref_msgs = 'Your sequence has not an ORF longer than 200 nt'

	else
		one_good_orf_minus = false
		more_than_one_minus = false
		one_good_orf_plus = false
		more_than_one_plus = false

		good_orfs_minus = []
		good_orfs_plus = []

		one_coding = false
		one_putative = false

		# orfs_array.sort! {|orf1,orf2| (orf1[2] - orf1[1]) <=> (orf2[2] - orf2[1])}
		orfs_array.each do |orf|

			# long = orf.length - 1
			if (orf[0])
			# if (long >= 200)
				(t_code,t_status)=testCode_exec(orf[0])
#						puts "name: #{name},t_status: #{t_status}, t_code: #{t_code}, stop_codon: #{orf[4]}, length: #{tc_fasta.length}, start: #{orf[1]}, end: #{orf[2]}, frame: #{orf[3]}\n\n"

				if (t_status != 'unknown')
					if (orf[3].to_i < 0)
						if (one_good_orf_minus == true)
							more_than_one_minus = true
							orf.push t_code
							orf.push t_status
							good_orfs_minus.push orf
						else
							one_good_orf_minus = true
							orf.push t_code #orf[5]
							orf.push t_status #orf[6]
							good_orfs_minus.push orf
						end
					elsif (orf[3].to_i > 0)
						if (one_good_orf_plus == true)
							more_than_one_plus = true
							orf.push t_code
							orf.push t_status
							good_orfs_plus.push orf
						else
							one_good_orf_plus = true
							orf.push t_code #orf[5]
							orf.push t_status #orf[6]
							good_orfs_plus.push orf
						end
					end
				end

				# if (t_code.to_f > ref_code) # cogemos el de mejor testcode
				# puts "name: #{name}, orf[0].length: #{orf[0].length}, ref_orf.length: #{ref_orf.length}, t_status: #{t_status}, one_coding: #{one_coding}\n\n"
				if (orf[0].length > ref_orf.length) and (t_status == 'coding') # cogemos el mayor de los coding
					# puts "compleeeeeeeeeeeeeeetttttttttttaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa"
					ref_code = t_code.to_f
					ref_name = name
					ref_orf = orf[0]
					ref_start = orf[1]
					ref_end = orf[2]
					ref_frame = orf[3]

					one_coding = true
					(ref_status,ref_msgs) = checking_beginning(orf[4],t_status,orf[1],tc_fasta,orf[2])

				elsif (one_coding == false) and (orf[0].length > ref_orf.length) and (t_status == 'putative_coding')
					# puts "putaaaaaaaaaaaaaaaaaaativeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee"
					ref_code = t_code.to_f
					ref_name = name
					ref_orf = orf[0]
					ref_start = orf[1]
					ref_end = orf[2]
					ref_frame = orf[3]

					one_putative = true
					(ref_status,ref_msgs) = checking_beginning(orf[4],t_status,orf[1],tc_fasta,orf[2])

				elsif (one_coding == false) and (one_putative == false)
					# puts "unknoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooown"
					ref_status = t_status
					ref_code = t_code.to_f
					ref_name = name
					ref_orf = orf[0]
					ref_start = orf[1]
					ref_end = orf[2]
					ref_frame = orf[3]

					ref_msgs = 'Bad testcode score'
					# ref_msgs = 'test code did not find a coding region in your sequence'
				end
				# puts "**name: #{name},ref_status: #{ref_status}, ref_code: #{ref_code}, length: #{tc_fasta.length}, ref_start: #{ref_start}, ref_end: #{ref_end}, ref_frame: #{ref_frame}\n\n"
				# puts "t_code: #{t_code}, t_status: #{t_status}"
			end
		end

		# vamos a preparar el mejor ORF y devolverlo
		(ref_start,ref_end) = corrige_frame(ref_frame,ref_start,ref_end)
		# puts "**name: #{name}, ref_start: #{ref_start}, ref_end: #{ref_end}, ref_frame: #{ref_frame}\n\n"
		
		# si encontramos más de un orf valido
		if (more_than_one_plus) or (more_than_one_minus)
			if (ref_frame > 0)
				if (more_than_one_plus)
					(ref_status,ref_code,ref_name,ref_start,ref_end,ref_frame,ref_orf,ref_msgs) = orf_fusion(good_orfs_plus,tc_fasta,name,ref_status,ref_code,ref_start,ref_end,ref_frame,ref_orf,ref_msgs)
					# if (ref_frame == 0)
					# 	ref_frame = 7
					# end
					# puts "merging ORFs with orf_fusion!!!!"
				end
			elsif (ref_frame < 0)
				if (more_than_one_minus)
					(ref_status,ref_code,ref_name,ref_start,ref_end,ref_frame,ref_orf,ref_msgs) = orf_fusion(good_orfs_minus,tc_fasta,name,ref_status,ref_code,ref_start,ref_end,ref_frame,ref_orf,ref_msgs)
					# if (ref_frame == 0)
					# 	ref_frame = -7
					# end
					# puts "merging ORFs with orf_fusion!!!!"
				end
			end
		end

		# puts "name: #{name},t_status: #{ref_status}, t_code: #{ref_code}, frame: #{ref_frame},start: #{ref_start}, end: #{ref_end}\n\n"

		if (ref_frame < 0)
			(kk1,kk2,ref_start2,ref_end2) = reverse_seq(tc_fasta,ref_frame,ref_start,ref_end)

			ref_start_ok = "#{ref_start2} (-#{ref_start})"
			ref_end_ok = "#{ref_end2} (-#{ref_end})"
		else
			ref_start_ok = ref_start
			ref_end_ok = ref_end
		end
	end

		return [ref_name,ref_code,ref_status,ref_start_ok,ref_end_ok,ref_frame,ref_orf,ref_msgs]

end

#testCode_exec(sequence) ⇒ Object

test code program functions #########



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# File 'lib/full_lengther_next/test_code.rb', line 703

def testCode_exec (sequence)

	sequence.downcase!
	basesOne = [0,0,0,0];
	basesTwo = [0,0,0,0];
	basesThree = [0,0,0,0];

	#for (j = 0; j < sequence.length; j = j + 3)

	0.step(sequence.length-1,3) do |j|
		if (sequence[j].chr == "g")
			basesOne[0] = basesOne[0] + 1;
		elsif (sequence[j].chr == "a")
			basesOne[1] = basesOne[1] + 1;
		elsif (sequence[j].chr == "t")
			basesOne[2] = basesOne[2] + 1;
		elsif (sequence[j].chr == "c")
			basesOne[3] = basesOne[3] + 1;
		else
		end
	end

					#for (j = 1; j < sequence.length; j = j + 3)
	1.step(sequence.length-1,3) do |j|
		if (sequence[j].chr == "g")
			basesTwo[0] = basesTwo[0] + 1;
		elsif (sequence[j].chr == "a")
			basesTwo[1] = basesTwo[1] + 1;
		elsif (sequence[j].chr == "t")
			basesTwo[2] = basesTwo[2] + 1;
		elsif (sequence[j].chr == "c")
			basesTwo[3] = basesTwo[3] + 1;
		else
		end
	end


	#for (j = 2; j < sequence.length; j = j + 3)
	2.step(sequence.length-1,3) do |j|
		if (sequence[j].chr == "g")
			basesThree[0] = basesThree[0] + 1;
		elsif (sequence[j].chr == "a")
			basesThree[1] = basesThree[1] + 1;
		elsif (sequence[j].chr == "t")
			basesThree[2] = basesThree[2] + 1;
		elsif (sequence[j].chr == "c")
			basesThree[3] = basesThree[3] + 1;
		else
		end
	end

	paramG = calcParam(basesOne[0],basesTwo[0],basesThree[0]);
	contentG = countBases(basesOne[0],basesTwo[0],basesThree[0]) / sequence.length.to_f;
	posProbG = usePosParam(paramG,"g");
	contProbG = useContParam(contentG,"g");
	paramA = calcParam(basesOne[1],basesTwo[1],basesThree[1]);
	contentA = countBases(basesOne[1],basesTwo[1],basesThree[1]) / sequence.length.to_f;
	posProbA = usePosParam(paramA,"a");
	contProbA = useContParam(contentA,"a");
	paramT = calcParam(basesOne[2],basesTwo[2],basesThree[2]);
	contentT = countBases(basesOne[2],basesTwo[2],basesThree[2]) / sequence.length.to_f;
	posProbT = usePosParam(paramT,"t");
	contProbT = useContParam(contentT,"t");
	paramC = calcParam(basesOne[3],basesTwo[3],basesThree[3]);
	contentC = countBases(basesOne[3],basesTwo[3],basesThree[3]) / sequence.length.to_f;
	posProbC = usePosParam(paramC,"c");
	contProbC = useContParam(contentC,"c");
	valueY = posProbG * 0.31 + contProbG * 0.15 + posProbA * 0.26 + contProbA * 0.11 + posProbT * 0.33 + contProbT * 0.14 + posProbC * 0.18 + contProbC * 0.12;
	valueY = ((valueY*1000.0).round/1000.0);

	# return 'The TestCode value is <b>' + valueY.to_s + '</b>, which indicates that the sequence ' + getConclusion(valueY) + '.';
	return [valueY, getConclusion(valueY)]
end

#type_fusion(prev_type, one_type) ⇒ Object

cuando se unen dos regiones de diferentes frames, nos dice de que tipo es la union, Complete, Internal, N-terminus…



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# File 'lib/full_lengther_next/test_code.rb', line 166

def type_fusion(prev_type,one_type)
	res_type = :Internal
	if (prev_type == :C_terminus) #-------------- C-terminus
			if (one_type == :N_terminus)
				res_type = :Internal
			elsif (one_type == :Internal)
				res_type = :Internal
			elsif (one_type == :Complete)
				res_type = :C_terminus
			end
	elsif (prev_type == :N_terminus) #-------------- N-terminus
		if (one_type == :C_terminus)
			res_type = :Complete
		elsif (one_type == :Internal)
			res_type = :N_terminus
		elsif (one_type == :Complete)
			res_type = :Complete
		end
	elsif (prev_type == :Internal) #-------------- Internal
		if (one_type == :C_terminus)
			res_type = :C_terminus
		elsif (one_type == :N_terminus)
			res_type = :Internal
		elsif (one_type == :Complete)
			res_type = :C_terminus
		end
	elsif (prev_type == :Complete) #-------------- Complete
		if (one_type == :C_terminus)
			res_type = :Complete
		elsif (one_type == :N_terminus)
			res_type = :N_terminus
		elsif (one_type == :Internal)
			res_type = :N_terminus
		end
	end
	return res_type
end

#uncomplete_orf_finder(seq) ⇒ Object

recorre cada uno de los frames y los pasa a generate_uncomplete_orf



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# File 'lib/full_lengther_next/test_code.rb', line 293

def uncomplete_orf_finder(seq)
	
	s = seq.seq_fasta.upcase
	f1 = s.split('').each_slice(3).map{|e| e.join}
	generate_uncomplete_orf(f1,1,seq)
	
	s.sub!(/^./,'')
	f2 = s.split('').each_slice(3).map{|e| e.join}
	generate_uncomplete_orf(f2,2,seq)
	
	s.sub!(/^./,'')
	f3 = s.split('').each_slice(3).map{|e| e.join}
	generate_uncomplete_orf(f3,3,seq)
	
	# vamos a por los ORFs de la cadena complementaria
	s = seq.seq_fasta.upcase
	s = s.complementary_dna
	
	f4 = s.split('').each_slice(3).map{|e| e.join}
	generate_uncomplete_orf(f4,-1,seq)
	
	s.sub!(/^./,'')
	f5 = s.split('').each_slice(3).map{|e| e.join}
	generate_uncomplete_orf(f5,-2,seq)
	
	s.sub!(/^./,'')
	f6 = s.split('').each_slice(3).map{|e| e.join}
	generate_uncomplete_orf(f6,-3,seq)
	
end

#useContParam(paramValue, base) ⇒ Object 



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# File 'lib/full_lengther_next/test_code.rb', line 828

def useContParam (paramValue,base)
	arrayOfCodingProb = [];
	codeProb = 0;
	if (base == "g")
		arrayOfCodingProb = [0.29,0.33,0.41,0.41,0.73,0.64,0.64,0.47,0.54,0.40]
	elsif (base == "a")
		arrayOfCodingProb = [0.21,0.81,0.65,0.67,0.49,0.62,0.55,0.44,0.49,0.28]
	elsif (base == "t")
		arrayOfCodingProb = [0.58,0.51,0.69,0.56,0.75,0.55,0.40,0.39,0.24,0.28]
	elsif (base == "c")
		arrayOfCodingProb = [0.31,0.39,0.44,0.43,0.59,0.59,0.64,0.51,0.64,0.82]
	end

	if (paramValue >= 0 and paramValue < 0.17)
		codeProb = arrayOfCodingProb[0];
	elsif (paramValue >=0.17 and paramValue < 0.19)
		codeProb = arrayOfCodingProb[1];
	elsif (paramValue >=0.19 and paramValue < 0.21)
		codeProb = arrayOfCodingProb[2];
	elsif (paramValue >=0.21 and paramValue < 0.23)
		codeProb = arrayOfCodingProb[3];
	elsif (paramValue >=0.23 and paramValue < 0.25)
		codeProb = arrayOfCodingProb[4];
	elsif (paramValue >=0.25 and paramValue < 0.27)
		codeProb = arrayOfCodingProb[5];
	elsif (paramValue >=0.27 and paramValue < 0.29)
		codeProb = arrayOfCodingProb[6];
	elsif (paramValue >=0.29 and paramValue < 0.31)
		codeProb = arrayOfCodingProb[7];
	elsif (paramValue >=0.31 and paramValue < 0.33)
		codeProb = arrayOfCodingProb[8];
	elsif (paramValue >=0.33)
		codeProb = arrayOfCodingProb[9];
	end

	return codeProb;
end

#usePosParam(paramValue, base) ⇒ Object 



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# File 'lib/full_lengther_next/test_code.rb', line 789

def usePosParam (paramValue,base)
	arrayOfCodingProb = [];
	codeProb = 0;
	if (base == "g")
		arrayOfCodingProb = [0.08,0.08,0.16,0.27,0.48,0.53,0.64,0.74,0.88,0.90]
	elsif (base == "a")
		arrayOfCodingProb = [0.22,0.20,0.34,0.45,0.68,0.58,0.93,0.84,0.68,0.94]
	elsif (base == "t")
		arrayOfCodingProb = [0.09,0.09,0.20,0.54,0.44,0.69,0.68,0.91,0.97,0.97]
	elsif (base == "c")
		arrayOfCodingProb = [0.23,0.30,0.33,0.51,0.48,0.66,0.81,0.70,0.70,0.80]
	end


	if (paramValue >= 0 and paramValue < 1.1)
		codeProb = arrayOfCodingProb[0];
	elsif (paramValue >=1.1 and paramValue < 1.2)
		codeProb = arrayOfCodingProb[1];
	elsif (paramValue >=1.2 and paramValue < 1.3)
		codeProb = arrayOfCodingProb[2];
	elsif (paramValue >=1.3 and paramValue < 1.4)
		codeProb = arrayOfCodingProb[3];
	elsif (paramValue >=1.4 and paramValue < 1.5)
		codeProb = arrayOfCodingProb[4];
	elsif (paramValue >=1.5 and paramValue < 1.6)
		codeProb = arrayOfCodingProb[5];
	elsif (paramValue >=1.6 and paramValue < 1.7)
		codeProb = arrayOfCodingProb[6];
	elsif (paramValue >=1.7 and paramValue < 1.8)
		codeProb = arrayOfCodingProb[7];
	elsif (paramValue >=1.8 and paramValue < 1.9)
		codeProb = arrayOfCodingProb[8];
	elsif (paramValue >=1.9)
		codeProb = arrayOfCodingProb[9];
	end

	return codeProb;
end

#window_walking(seq) ⇒ Object

gnuplot must be installed



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# File 'lib/full_lengther_next/test_code.rb', line 588

def window_walking(seq)
	
	tcode_array = []
	y1=[]
	y2=[]
	
	s = seq.seq_fasta.upcase
	(s.length-200).times do |i|
		(t_code,t_status)=testCode_exec(s[i..i+199])
		y1.push t_code
	end
	
	tcode_array_rc = []
	
	src = s.complementary_dna
	(src.length-200).times do |i|
		(t_code,t_status)=testCode_exec(src[i..i+199])
		# puts "#{i}-#{i+199}"
		# puts t_status
		# puts t_code
		puts src[i..i+199]
		y2.push t_code
	end
	
	# Create lines plot
  p=ScbiPlot::Lines.new('lines.png','title')
  x=(1..src.length-200).entries
  p.add_x(x)
	
	# puts "x_length: #{src.length-200} #{x}"
	# puts "x: #{x.length}, y: #{y1.length}"
	p.add_series('serie0', y1)

	p.do_graph
	
end