gene_assembler 0.0.9

data/lib/gene_assembler/hsp.rb

@@ -0,0 +1,100 @@
+class Hsp
+	attr_accessor :q_beg, :q_end, :s_beg, :s_end, :align_len, :score, :ident, :gaps, :type 
+	def initialize (q_beg, q_end, s_beg, s_end, align_len, score, ident, gaps)
+  		@q_beg=q_beg #Inicio en query
+		@q_end=q_end #Fin en query
+		@s_beg=s_beg #Inicio en subject
+		@s_end=s_end #Fin en subject
+		@align_len=align_len #Tamaño de la secuencia alineada
+		#@bit_score=bit_score
+		@score=score
+		@ident=ident
+		@gaps=gaps
+		@type=nil
+	end 
+
+	def compare(hsp) #Compara hsps distintintos a nivel del subject para saber si son el mismo
+		coverage=0
+		if self.s_beg==hsp.s_end && self.s_end==hsp.s_end
+			coverage=1
+		elsif self.s_beg>=hsp.s_beg && self.s_end<hsp.s_end #Caso de q el self este dentro de hsp
+			coverage=1
+		elsif self.s_beg<=hsp.s_beg && self.s_end>hsp.s_beg && (self.s_end-hsp.s_beg).abs>1
+			ext=self.s_end-hsp.s_beg*1.00 # El producto obliga a usar la clase float para impedir q trunque el resultado
+			coverage=ext/(self.s_end-self.s_beg)
+		elsif self.s_beg<hsp.s_end && self.s_end>=hsp.s_end && (self.s_beg-hsp.s_end).abs>1 #Ultima condicion impide q de como mismo exon el compartir un aa q realmente esta partido entre 2 exones
+			ext=hsp.s_end-self.s_beg*1.00
+			coverage=ext/(self.s_end-self.s_beg)			
+		end
+		return coverage
+	end
+
+  def compare_q(hsp) #Compara hsps distintintos a nivel del query para saber si son el mismo
+    coverage=0
+    if self.q_beg==hsp.q_end && self.q_end==hsp.q_end
+      coverage=1
+    elsif self.q_beg>=hsp.q_beg && self.q_end<hsp.q_end #Caso de q el self este dentro de hsp
+      coverage=1
+    elsif self.q_beg<=hsp.q_beg && self.q_end>hsp.q_beg && (self.q_end-hsp.q_beg).abs>1
+      ext=self.q_end-hsp.q_beg*1.00 # El producto obliga a usar la clase float para impedir q trunque el resultado
+      coverage=ext/(self.q_end-self.q_beg)
+    elsif self.q_beg<hsp.q_end && self.q_end>=hsp.q_end && (self.q_beg-hsp.q_end).abs>1 #Ultima condicion impide q de como mismo exon el compartir un aa q realmente esta partido entre 2 exones
+      ext=hsp.q_end-self.q_beg*1.00
+      coverage=ext/(self.q_end-self.q_beg)      
+    end
+    return coverage
+  end
+
+	
+	def length_q #Longitud del hsp en la query
+		length=@q_end-@q_beg
+		return length
+	end
+	
+	def rev(length_hsp) # Cambia coordenadas de reversas a directas
+		@q_beg=length_hsp-@q_beg #Inicio en query
+		@q_end=length_hsp-@q_end #Fin en query
+		@reversed=FALSE
+	end
+	
+	def within?(hsp,long) #Mira si un hsp esta dentro de otro o si hay overlap parcial entre los mismos
+		over=0
+		if self.q_beg<=hsp.q_beg && self.q_end>=hsp.q_end
+			over=1
+		end
+		if self.s_beg<=hsp.s_beg && self.s_end>=hsp.s_end
+			over=1
+		end
+		if over == 0
+			self_coverage=(self.s_end-self.s_beg)*1.00/long
+			hsp_coverage=(hsp.s_end-hsp.s_beg)*1.00/long
+			if hsp_coverage>(1-self_coverage) #Si el coverage del hsp en mayor que el resto que deja el self, se da como overlap
+				over=1
+			end
+		end
+		return over
+	end
+	
+	def modified_coordenates(add)
+  	@q_beg+=add
+		@q_end+=add
+	end
+	
+	def rev_coord(contig_length)
+		puts '---------------------------------'
+		puts @q_beg.to_s+' '+@q_end.to_s
+		@q_beg=contig_length-@q_beg+1
+		@q_end=contig_length-@q_end+1
+		puts @q_beg.to_s+' '+@q_end.to_s
+	end
+	
+	def overlap_with(last_hsp)
+	  overlap=0
+	  diference=self.s_beg-last_hsp.s_end
+	  #puts "#{self.s_beg} - #{last_hsp.s_end} = #{diference}"
+	  if diference<0
+	    overlap=diference
+	  end
+	  return overlap
+	end
+end

data/lib/gene_assembler/other_functions.rb

@@ -0,0 +1,228 @@
+require 'scbi_fasta'
+
+def mapping(contigs,gene_array,map_path) #Relaciona un archivo sam con un contig, cuantifica nº lecturas por exon
+	# Mapping
+	#--------------------------------------------------------------
+	contigs.each do |contig|
+		ruta=File.join(map_path,"#{contig.name}.sam")
+			 
+		# Parse mapping & exon valoration
+		#--------------------------------------------------------------
+		seq_map=[]
+		n_reads=0
+		if File.exists?(ruta)
+			contig.length.times do |x|
+				seq_map  <<  0	
+			end
+			map_file=File.open(File.join(ruta), 'r')
+			map_file.each do |line|
+				fields=line.split
+				if fields[0]!~/[@]/
+					n_reads+=1
+					#puts "#{fields[3]}\t#{fields[5]}"
+					start_map=fields[3].to_i-1
+				  end_map=start_map-1
+					fields[5].split(/[^\d]/).each{|e| end_map+=e.to_i}
+					#puts "#{start_map}\t#{end_map}"
+					#puts seq_map[start_map..end_map].inspect
+					seq_map.each_with_index do |item,a|
+						if a>=start_map
+							seq_map[a]+=1
+						end
+						if a>end_map
+							break
+						end
+					end
+				end
+			end
+			#puts seq_map.inspect
+
+			# Exon valoration
+			#-----------------------------------------------------------
+			exon_stadistic=[]
+			contig.hits.first.hsps.each do |hsp|
+				exon=seq_map[hsp.q_beg-1..hsp.q_end-1]
+				value=0
+				exon.each{|e| value+=e}
+				exon_stadistic << (value*100.0/n_reads/exon.length).round(2)
+			end
+			#puts exon_stadistic.inspect
+			y=contigs.index(contig)
+			x=gene_array[y].index(1)
+			exon_stadistic.each_with_index do |item,b|
+				gene_array[y][x+b]=item
+			end
+			seq_map=[]	
+		end
+	end #end contigs.each
+
+	if $verbose
+		puts "\nGENE ARRAY - EXON VALUATED"
+		gene_array.each_with_index do |fila,c|
+			print "#{contigs[c].name.center(24)} "
+			fila.each do |item|
+				print "#{item.to_s}\t"
+			end
+			puts "\n"
+		end
+	end
+
+	contigs.each do |contig|
+		puts '...................'
+		contig.indices
+	end
+	puts "\n"
+end
+
+def length2D(array) # Devuelve la longitud maxima que tenga un conjunto de arrays
+	length=0
+	array.each do |item|
+		item_length=item.length
+		if item_length>length
+			length=item_length
+		end
+	end
+	return length
+end
+
+def parse_contig_index(gene_array,contigs) #Comprueba codones start- stop en contigs que contengan el primer o el ultimo exon
+	exons_model=length2D(gene_array)
+	gene_array.each_with_index do |contig,i|
+		start=nil #Desconocido
+		if contig.first >0 #Comprueba si el contig tiene el primer exon
+			start=contigs[i].start_codon_search
+		end
+		stop=nil #desconocido
+		#if contig.length==exons_model #Comprueba si el contig posee el ultimo exon
+			stop=contigs[i].stop_codon_search
+		#end
+		if start==TRUE && stop==TRUE
+			contigs[i].completed=TRUE
+		elsif start==TRUE
+			contigs[i].completed='start'
+		elsif stop==TRUE
+			contigs[i].completed='stop'
+		else
+			contigs[i].completed=FALSE
+		end
+	end
+end
+
+def sides_recovery(contigs) # Toma de un conjunto de contigs un contig con señal de stop y un contig con señal de inicio
+	start=nil
+	stop=nil
+	contigs.each do |contig|
+		if contig.completed=='start'
+			if start.nil?
+				start=contig
+			else
+				if start.hits.first.hsps.first.score<contig.hits.first.hsps.first.score
+					start=contig
+				end
+			end
+		end
+		if contig.completed=='stop'
+			if stop.nil?
+				stop=contig
+			else
+				if stop.hits.first.hsps.first.score<contig.hits.first.hsps.first.score
+					stop=contig
+				end
+			end
+		end
+	end
+	return start,stop
+end
+
+def sides_add(contigs,start,stop) #Añade contigs con señal de stop-start si no existen en el array contigs
+	beg=TRUE
+	ends=TRUE
+	contigs.each do |contig|
+		if contig.completed=='start'||contig.completed==TRUE
+			beg=FALSE
+		end
+		if contig.completed=='stop'||contig.completed==TRUE
+			ends=FALSE
+		end		
+	end
+	if beg && !start.nil?
+		b=[]
+		b << start
+		contigs=b.concat(contigs)
+	end
+	if ends && !stop.nil?
+		e=[]
+		e << stop
+		contigs.concat(e)
+	end
+	return contigs
+end
+
+def cluster_filter(gene_array,cluster,length)# Elimina contigs de cluster y gene_array que tengan etiqueta de stop y solo tengan un hsp
+	cluster.each_with_index do |contig,i|
+		if contig.completed=='stop' 
+			if contig.hits.first.hsps.last.s_end-contig.hits.first.hsps.last.s_beg<length && contig.hits.first.hsps.count==1
+				cluster[i]=nil
+				gene_array[i]=nil
+			end
+		end
+	end
+	cluster.compact!
+	gene_array.compact!
+	return gene_array,cluster
+end
+
+def coord_prot(last_contig_hsp, current_contig_hsp) #Devuelve la diferencia de posicion de dos contigs dados en base a su posicion en la proteina
+	add=last_contig_hsp.q_beg-current_contig_hsp.q_beg+3*(current_contig_hsp.s_beg-last_contig_hsp.s_beg) #primera parte del sumando representa la diferencia debida a la longitud de los contigs, la segunda parte representa la diferencia de tamaño del hsp
+	return add
+end
+
+def fasta_hash(path)
+  parse_seqs=FastaFile.new(path)
+  seqs={}
+  parse_seqs.each do |contig,seq_fasta|
+    seqs[contig]=seq_fasta
+  end
+  return seqs
+end
+
+def html_header(file,title)
+  file.puts '<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">',
+            '<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">',
+            '<head>',
+            '<meta http-equiv="content-type" content="text/html;charset=UTF-8" />',
+            '<title>'+title+'</title>',
+            '</head>',
+            '<body>'
+end
+
+def html_footer(file)
+  file.puts '</body>',
+            '</html>'
+end
+
+def html_table_header(file, border, headers) #headers es un array
+  file.puts '<table border="'+border.to_s+'">',
+            '<tr>'
+  headers.each do |header|
+    file.puts '<th>'+header+'</th>'
+  end                    
+  file.puts '</tr>'
+end
+
+def html_row(file, cells) #Cells muts be a array
+	file.puts '<tr>'
+	cells.each do |cell|
+		file.puts "<td>#{cell}</td>"
+	end
+	file.puts '</tr>'
+end
+
+def html_link(text, link)
+	text_linked='<a href="'+link+'">'+text.to_s+'</a>'
+	return text_linked
+end
+
+def html_table_footer(file)
+  file.puts '</table>'
+end

data/lib/gene_assembler/parser.rb

@@ -0,0 +1,25 @@
+require 'dataset'
+
+class Parser
+	attr_accessor :dataset
+	def initialize(file,type=nil)
+    @file=file
+		@dataset=create_dataset
+		data=parse_file(file) #Se crea objeto de datos para cargar dataset
+		load_dataset(data) #Se rellena dataset con la informacion contenida en data
+	end
+
+	def create_dataset
+		dataset=Dataset.new('unknown')#No se usa
+		return dataset
+	end
+	
+	def parse_file(file)
+		
+	end
+	
+	def load_dataset(data)
+		
+	end
+
+end

data/lib/gene_assembler/parser_blast.rb

@@ -0,0 +1,12 @@
+require 'blast_type_parser'
+require 'scbi_blast' #Si falla, buscar e instalar tb 'gem install xml-simple' de la q depende
+
+
+class ParserBlast < BlastTypeParser
+
+  def parse_file(file)
+    blast=BlastTableResult.new(file)
+    return blast
+  end
+
+end	

data/lib/gene_assembler/parser_exonerate.rb

@@ -0,0 +1,16 @@
+require 'exonerate_result'
+require 'blast_type_parser'
+
+class ParserExonerate < BlastTypeParser
+
+  def parse_file(file)
+    exonerate=ExonerateResult.new(file,@all)
+    return exonerate
+  end
+
+	def populate_extra_atributes(contig,item) #Añade los frameshift localizados x el exonerate
+		   	contig.q_frameshift=item.q_frameshift
+	    	contig.s_frameshift=item.s_frameshift
+	end
+
+end	

data/lib/gene_assembler/rebuild.rb

@@ -0,0 +1,975 @@
+require 'dataset'
+require 'other_functions'
+require 'report_gff'
+require 'fileutils'
+
+class Rebuild
+	def initialize(dataset,dataset_uni_hsp,path) #La clase ha de recibr objetos dataset
+		@dataset=dataset
+		@dataset_uni_hsp=dataset_uni_hsp
+		@path=path
+		@db_seqs=fasta_hash(path[:exonerate_db])
+	end
+
+	###############################################################################################################
+	# MAIN METHOD 
+	###############################################################################################################
+	def rebuild(options) #Genera contigs modelo,gff y busca pseudogenes
+		gff_dataset_model=Dataset.new(:mix) #Object for save info of GeneAssembler's output
+		gff_dataset=Dataset.new(:mix) #Object for save info of GeneAssembler's output
+		file_error=File.open(@path[:error],'w')
+		file_web=web_header(options[:web],@path[:html])
+		sequences_hash={}
+		gene_name=nil
+		model=nil
+		statistics={:genes => 0, :total_recovered => 0, :total_overlap => 0, :total_fragmentation => 0}
+		puts "\nMODELING GENE",'*******************************************'
+		@dataset.each_cluster{|cluster|
+			begin
+				if !cluster.nil?
+					gene_name=cluster.first.first_hit.name
+				end
+				cluster_complete=cluster.dup
+				model, length_model, length_cluster = iterative_modeling_gene_w_reference(cluster,@dataset.references_hash,options[:rebuild],sequences_hash) #Realiza la reconstruccion del gen (alineado,descarte y montaje del gen)
+
+	  			# GeneAssembler output (gff for Gbrowse)
+	  			#--------------------------------------------------------
+	  			if !model.nil?
+	  				#Format Contigs children of model				
+	  				gff_dataset.clr_contigs
+	  				gff_dataset.transfer_contigs(cluster_complete)
+	  				gff_dataset.transfer_n_contigs_def_hit_type(@dataset_uni_hsp,cluster,'pseudogene',50) #Transferir pseudogenes al report
+	  				
+					# Convertir arrays a contig y ajustar alineamiento añadiendo Ns
+	  				model=correct_model(model, length_model, gff_dataset, sequences_hash)
+
+	  				# Comprobaciones en el modelo
+	  				exones=model.exones_s.length # N exones
+	  				puts 'Exones: '+ exones.to_s
+	  				recovered=recover_test(model)
+	  				overlap=overlap_test(model)
+	  				fragmentation=((length_cluster-1.00)/exones).round(2)
+	  				puts 'Fragmentation: ' + fragmentation.to_s
+  				
+	  				# HTML index
+	  				if !file_web.nil?
+	  					gene_link=html_link(model.first_hit.name, @path[:gbrowse_link]+model.first_hit.name)
+	  					html_row(file_web, [gene_link, cluster.first.first_hit.s_length, exones, recovered, overlap, fragmentation])
+					end
+  			
+	  				#Format Model for Gbrowse
+	  				gff_dataset_model.clr_contigs
+	  				format_model(model) #Añade la particula _gene al modelo
+	  				gff_dataset_model.transfer_contigs(model)
+  				
+	  				#Write
+	  				write_gbrowse_gff(gff_dataset_model, gff_dataset, @path[:gff], model.name)
+  				
+	  				#General statistics
+	  				statistics[:genes]+=1
+	  				statistics[:total_recovered]+=recovered
+	  				statistics[:total_overlap]+=overlap
+	  				statistics[:total_fragmentation]+=fragmentation
+	  			end
+			rescue Exception => e
+				gene_error(e, gene_name, file_error, cluster_complete, model)
+			end
+			puts '* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *'		
+		}
+		file_error.close
+		web_body(file_web)
+
+		puts	"\nFINAL STATISTICS\n",
+			'Recovered genes: '+ statistics[:genes].to_s,
+			'Mean recover: ' + (statistics[:total_recovered]/statistics[:genes]).to_s,
+			'Mean overlap: ' + (statistics[:total_overlap]/statistics[:genes]).to_s,
+			'Mean fragmentation: ' + (statistics[:total_fragmentation]/statistics[:genes]).to_s
+		write_model_fasta(sequences_hash,@path[:fasta])
+	end
+	################################################################################################################################
+	# end main method 
+	################################################################################################################################
+  
+  def iterative_modeling_gene_w_reference(cluster,references_hash,options,sequences_hash)
+    # Model atributes
+    model=nil
+    length=0
+    seq=nil
+    cluster_length=0
+    length_cluster=0
+    prot_reference=cluster.first.first_hit.name
+    array_references=references_hash[prot_reference]
+
+    # Model parameters
+    recover=0
+    overlap=0
+
+    #Modelo de gen en ciego
+    if $verbose
+      puts "\n",'||||||||||  BLIND MODELING  ||||||||||'
+    end
+    model, length, seq, length_cluster= modeling_gene(cluster.dup,nil,options)
+
+    recover, overlap=eval_model(model.dup, length)
+
+    if $verbose
+      puts "\nRecover: #{recover} Overlap: #{overlap}"
+    end
+    
+    guided=FALSE
+    #Modelo de gen guiado
+    if !array_references.nil?
+      array_references.each do |ref|
+        if $verbose
+          puts "\n",'||||||||||  GUIDED MODELING  ||||||||||'
+        end
+  
+        guided_model, guided_length, guided_seq, guided_length_cluster = modeling_gene(cluster.dup,ref,options)
+        if guided_model.nil? # Si algun modelo sale mal se ignora
+          next
+        end
+        guided_recover, guided_overlap= eval_model(guided_model.dup, guided_length)
+        if $verbose
+          puts "\nRecover: #{guided_recover} Overlap: #{guided_overlap}"
+        end
+        
+        #Arbol de decisiones
+        if guided_overlap <= 15 #Si el overlap es menor del 15 %
+          if guided_overlap >= overlap-overlap*0.05 && guided_overlap <= overlap+overlap*0.05 # A mismo overlap
+            if guided_recover > recover
+              guided=TRUE
+            end        
+          else # A distinto overlap
+            recover_dif=guided_recover-recover
+            if recover_dif < 0  # Si el guided_model tiene menos recuperacion q el anterior
+              if recover_dif.abs >= overlap-overlap*0.05 && recover_dif.abs <= overlap+overlap*0.05 #Si la reduccion de la recuperacion se debe a la desaparicion del overlap
+                guided=TRUE
+              end
+            elsif recover_dif> guided_overlap+guided_overlap*0.05 # Comprobar que la diferencia de recover no se debe a u aumento del overlap en la misma magnitud
+              guided=TRUE      
+            end
+          end
+        elsif guided_overlap < overlap # Quedarnos siempre con los overlap mas bajos aun en situacion de overlap alto
+          guided=TRUE
+        end
+        
+        if guided
+          model=guided_model
+          length=guided_length
+          seq=guided_seq
+          length_cluster=guided_length_cluster
+          recover=guided_recover
+          overlap=guided_overlap
+        end
+      end
+    end
+    
+    sequences_hash[prot_reference]=seq    
+    return model, length, length_cluster
+  end
+  
+  def eval_model(local_model, length)#modifica model asi q se le ha de pasar una copia
+    recover=0
+    overlap=0
+    if local_model.class.to_s=='Array'
+      local_model=array_contigs_to_contig(local_model)
+      local_model.length=length
+    end
+    recover=recover_test(local_model,FALSE)
+    overlap=overlap_test(local_model,FALSE)    
+    return recover, overlap
+  end
+  
+	def modeling_gene(cluster, reference, rebuild) #Funcion que devuelve un objeto contig con el modelo de gen, los contigs q se han seleccionado y genera un gff del modelo
+		model=nil
+		model_length=nil
+		seq=nil
+		length_cluster=0
+		# Reduccion iterativa de los contig para seleccionar los que van a formar parte del modelo de gen, elimina fragmentos menores que se puedan tomar como nuevos exones
+		#--------------------------------------------------------------------------------------------------
+		gene_array_length_before=nil
+		continue=TRUE
+		gene_array=[]
+			
+		while continue
+		      cluster,gene_array=gene_array_and_compact(rebuild,cluster,reference)
+		      gene_array_length_after=length2D(gene_array)
+		      if gene_array_length_after == gene_array_length_before
+		        continue=FALSE
+		      end
+		      gene_array_length_before=gene_array_length_after
+		end
+    		length_cluster=cluster.length
+
+		# Modelado del gen
+		#----------------------------------------------------
+		if rebuild && !cluster.empty? && !gene_array.empty?
+			if cluster.length >1
+				cluster_comp=contig_compact(cluster) #Fusiona contigs contiguos y devuelve el array correspondiente
+			else
+				cluster_comp=cluster
+			end
+			if !cluster_comp.nil?
+				model, model_length, seq=gene_model_cut(cluster_comp, reference)
+			else
+				puts cluster.first.first_hit.name+"\tGENE MODEL ABORTED"
+			end
+		end
+		return model, model_length, seq, length_cluster
+	end
+
+  def gene_array_and_compact(rebuild,cluster,reference)
+    # Contruir array de exones (a partir del cluster) con los hsps de forma que los solapantes se alineen en las mismas columnas
+    #---------------------------------------------------------------------------------------------------------------------------
+    if rebuild
+      gene_array,gene_array_introns=build_gene_array(cluster,reference) #Con referencia
+      if $verbose
+        gene_exons=gene_stadistics(gene_array)
+        gene_stadistics_report(gene_exons,'EXONS')
+        gene_introns=gene_stadistics(gene_array_introns)
+        gene_stadistics_report(gene_introns,'INTRONS')
+      end
+    end
+  
+    # Seleccion de contigs para modelado de gen
+    #-----------------------------------------------------
+    if $verbose #Info cluster before compact array contigs
+      gene_array_report(gene_array,cluster,rebuild)
+    end
+    if rebuild
+      gene_compact(gene_array,cluster) #Se descartan los contigs redundantes y quedan aquellos que cubren todo el gen para formar el modelo
+    end
+    if $verbose && rebuild #Info cluster after compact array contigs
+      gene_array_report(gene_array,cluster,rebuild)
+    end
+    return cluster, gene_array
+  end
+  
+  def add_uni_hsp(model,cluster)#Compara contigs uni-hsp con contig modelo para determinar pseudogenes
+    contigs_uni_hsp=''
+    is_contig=0
+    pseudogenes=[]
+    @clusters_uni_hsp.each do |contigs|
+      if contigs.first.first_hit.name==cluster.first.first_hit.name
+        contigs_uni_hsp=contigs
+        is_contig=1
+        break
+      end
+    end
+    
+    if is_contig==1 #Si se ha encontrado contigs uni-hsp se realiza la comparacion
+      if model.class.to_s!='Array'
+        model=[model]
+      end
+      model.each do |item|
+        contigs_uni_hsp.each do |contig|
+          start,exons=item.compare(contig)
+          if exons>1 && !pseudogenes.include?(contig)
+            pseudogenes << contig
+          end
+        end
+      end
+    end
+  	return pseudogenes
+  end
+  
+	def build_gene_array(contigs,reference=nil) #GEnera un array que representa la posicion relativa de todos los contigs entre si a nivel de los exones y de intrones
+		gene_array=[]
+		gene_array_introns=[]
+		last_contig=''
+		if !reference.nil?
+			last_contig=reference
+		end
+		contigs.each do |contig|
+				array_contig=[]
+				array_contig_introns=[]
+				n_exon=contig.first_hit.hsp_count #Contamos cantidad de hsps en el contig
+				#Determinar posiciones vacias
+				if !gene_array.empty?||reference 
+					first_exon,ex=contig.compare(last_contig) #Comparamos el contig actual con el que se ha estudiado en la iteracion anterior
+					if reference && first_exon==-1 # Abortar alineamiento cuando un contig no coincide con la referencia
+					  if $verbose
+					    puts "\n#{contig.name} alignment step OUT OF RANGE"
+					  end
+					  gene_array=[]
+					  gene_array_introns=[]
+					  break
+					end
+					if first_exon==-1
+						gene_array.last.count.times do #Posiciones vacias cuando NO hay overlapping
+							array_contig << 0 # Marca ausencia de exon para esa posicion
+							array_contig_introns << 0 # Marca ausencia de intron para esa posicion
+						end
+					else
+						if reference # ASignamiento de la posicion del contig respecto a la referencia
+							void_positions=first_exon
+						else
+							void_positions=first_exon+gene_array.last.count(0)
+						end
+						void_positions.times do #Posiciones vacias cuando HAY overlapping
+							array_contig << 0
+							array_contig_introns << 0
+						end
+					end
+				end
+				#Agregar exones e intrones del contig
+				exones=contig.exones_s
+				introns=contig.intrones_q
+				array_contig << exones # Marca presencia de exon para esa posicion
+				array_contig_introns << introns # Marca presencia de exon para esa posicion
+				gene_array << array_contig.flatten!
+				gene_array_introns << array_contig_introns.flatten!
+				if reference.nil?
+					last_contig=contig
+				end
+		end
+		return gene_array, gene_array_introns
+	end
+
+	def gene_stadistics(gene_array) #Calcula el nº exones diferentes que hay por cada posicion del gene_array
+		exons=[]
+		length=length2D(gene_array)
+		length.times do |column|
+			exon=[]
+			gene_array.each_with_index.each do |item,row|
+				if !exon.include?(gene_array[row][column]) && gene_array[row][column]!=0
+					exon << gene_array[row][column]
+				end
+			end
+			exons << exon
+		end
+		exons_stadistic=[]
+		exons.each do |ex|
+			exons_stadistic << ex.compact.length
+		end
+		return exons_stadistic	
+	end
+	
+	def gene_stadistics_report(exons_stadistic,tag) #Muestra estadisticas de intrones o exones
+		print "\n#{tag}\t"
+		exons_stadistic.each do |item|
+			print "#{item}\t"
+		end
+		print "\n"
+	end
+	
+	def gene_array_report(gene_array,contigs,act_array) #Muestra el array de la funncion build_gene_array y una representacion de las secuencias
+		if act_array 
+			puts "\nGENE ARRAY"
+			gene_array.each_with_index do |fila,c|
+				print "#{contigs[c].name.center(24)}\t "
+				print "#{contigs[c].completed}\t"
+				fila.each do |item|
+					print "#{item}\t"
+				end
+				puts "\n"
+			end
+		end
+		
+		puts "\nMAP"
+		contigs.each do |contig|
+			print "#{contig.name.center(25)}"
+			print contig.draw
+		end
+	end
+	
+	def gene_compact(gene_array, contigs) # Generacion modelo del gen quitando todas las secuencias redundantes posibles
+		gene_array.each_with_index do |contig,c1|
+			if !contig
+				next
+			end
+			c1_len=contig.length
+			n_exons=contig.count{|x| x>0}
+			gene_array.each_with_index do |contig2,c2|
+				if !contig2 ||c1==c2 #Saltamos contigs a nil o autocomparacion
+					next
+				end
+				c2_len=contig2.length
+				
+				# IGUAL
+				if c1_len==c2_len
+					if contig2.count{|x| x>0}==n_exons
+						if contigs[c1].first_hit.first_hsp.score>=contigs[c2].first_hit.first_hsp.score
+							gene_array[c2]=nil
+							contigs[c2]=nil
+						else 
+							gene_array[c1]=nil
+							contigs[c1]=nil
+							break
+						end
+					elsif contig2.count{|x| x>0}>n_exons 
+						gene_array[c1]=nil
+						contigs[c1]=nil
+						break
+					else
+						gene_array[c2]=nil
+						contigs[c2]=nil
+					end
+	
+				# MAYOR QUE
+				elsif c1_len>c2_len
+					if contig.count(0)<=contig2.count(0)
+						gene_array[c2]=nil
+						contigs[c2]=nil
+					end
+	
+				# MENOR QUE
+				elsif c1_len<c2_len
+					if contig.count(0)==contig2.count(0)
+						gene_array[c1]=nil
+						contigs[c1]=nil
+						break
+					end
+				end
+			end #end contig2
+		end #end contig
+		gene_array.compact!
+		contigs.compact!
+	end
+	
+	def contig_compact(contigs) # Toma un conjunto de contigs, busca los q son correlativos, los fusiona, pasa por el exonerate y devuelve un array con los nuevos contig
+		cn_def=[]
+		cn_backup=contigs.dup
+		#Determinar contigs a fusionar
+		cn_to_merge=[]
+		s_end=nil
+		last_position_ref=nil
+		position_overlap=nil
+		last_contig=nil
+		fusion=[]
+		contigs.length.times do
+			fusion << FALSE
+		end
+		#Marcaje de contigs correlativos no solapantes
+		contigs.each_with_index do |contig,i|
+			if i>0			
+	      diference=contig.first_hit.first_hsp.s_beg-s_end
+				if diference==0 || diference==1
+					fusion[i]=TRUE
+				end
+			end
+			s_end=contig.first_hit.last_hsp.s_end
+		end
+		
+		if fusion.include?(TRUE)
+			
+  		#Construccion array contigs a fusionar y guardado de los solapantes
+  		fusion_contigs=[]
+  		count=0	# Marca la posicion de las fusiones	
+  		fusion.each_with_index do |cont,i|
+  			if cont
+  				if !fusion_contigs.include?(contigs[i-1])
+  					fusion_contigs << contigs[i-1]
+  				end
+  				if !fusion_contigs.include?(contigs[i])
+  					fusion_contigs << contigs[i]
+  				end
+  			else
+  				if !fusion_contigs.empty?#Marcar fusiones
+  					cn_to_merge << fusion_contigs
+  					fusion_contigs=[]
+  					cn_def << count
+  					count+=1
+  				end
+  				if !fusion[i+1]||fusion[i+1].nil?#Guardar contigs que no participan en las fusiones
+  					cn_def << contigs[i]
+  				end
+  			end
+  			if i+1==fusion.length && !fusion_contigs.empty? #Control fin de bucle
+  				cn_to_merge << fusion_contigs
+  				cn_def << count
+  				count+=1
+  			end
+  		end
+  		
+  		#Generar fasta de los contig fusionados
+  		contigs_merge=contigs_seq_merge(cn_to_merge)
+  		if !contigs_merge.empty?
+    		temp=File.open(File.join(@path[:local],contigs.first.first_hit.name+'.fasta'),'w')
+    		contigs_merge.each_with_index do |seq,i|
+    			temp.puts ">Fusion_#{i}\n#{seq}"
+    		end
+    		temp.close
+  
+    		temp_db=File.open(File.join(@path[:local],contigs.first.first_hit.name+'.db'),'w')
+    		temp_db.puts ">#{contigs.first.first_hit.name}\n#{@db_seqs[contigs.first.first_hit.name]}"
+    		temp_db.close
+    		
+      end
+  		
+  		#Exonerating
+  		cmd="exonerate -q #{File.join(@path[:local],contigs.first.first_hit.name+'.db')} -t #{File.join(@path[:local],contigs.first.first_hit.name+'.fasta')} -Q protein -T dna -m protein2genome --percent 1 --showalignment 0 --useaatla 1 --showvulgar > #{File.join(@path[:local],contigs.first.first_hit.name+'.ex')}" #LINUX command line
+  		system(cmd)
+  		
+  		#Parsing exonerate
+  		local = ParserExonerate.new('contig','nucleotide_match', File.join(@path[:local],"#{contigs.first.first_hit.name}.ex"))
+  		store_local_ex = local.dataset
+  	  #store_local_ex.each_contig {|ite| puts ite.name+' '+ite.first_hit.name; ite.indices} 
+  		store_local_ex.score_correction(30)
+  		#puts "#{store_local_ex.contig_count}\t#{contigs_merge.length}"
+  		if store_local_ex.contig_count==contigs_merge.length
+  			#Recuperar atributos en contigs y cargar array con contigs def
+  			store_local_ex.each_contig_with_index{|contig,i|
+  				contig.seq=contigs_merge[i]
+  				contig.length=contigs_merge[i].length
+  				contig.first_hit.s_length=contigs.first.first_hit.s_length
+  				cn_def.each_with_index do |contig_def,j| # Busqueda de la posicion de la fusion y asignacion en el array de contigs definitivos
+  					if contig_def==i
+  						cn_def[j]=contig
+  					end
+  				end
+  			}
+  		else
+  			cn_def=cn_backup
+  		end
+		else
+		  cn_def=contigs
+		end
+
+		return cn_def
+
+	end#def
+	
+	def contigs_seq_merge(contigs) #Devuelve un array con las secuencias fusionadas a partir del array contigs donde se le proporciona los arrays a fusionar
+		cn=[]
+		seq=''
+		contigs.each do |contigs_to_merge|
+			contigs_to_merge.each do |contig|
+				if seq.empty?
+					seq=contig.seq
+				else
+					seq=seq+'n'*10+contig.seq
+				end
+			end
+			cn << seq
+			seq=''
+		end
+		return cn
+	end
+
+	def gene_model_cut(contigs, reference=nil) #Genera un modelo por corte y empalme de contigs, genera un gff y devuelve un array con objetos contig
+		q_beg=[]
+		q_end=[]
+		s_beg=[]
+		s_end=[]
+		seq=[]
+		last_contig=nil
+		last_score=0
+		length_model=0
+		multiple_lengths=[]
+		add_length=TRUE
+		add_last=0
+		last_position_ref=nil
+		last_position=nil
+		lengthy=[]
+		out_of_range=FALSE
+		contigs.each do |contig|
+			score = contig.first_hit.first_hsp.score/contig.length*contig.exon_acumulative
+			n_exones = contig.first_hit.hsp_count
+			
+			# FIRST CONTIG
+			#-------------------------------------------------------
+			if last_contig.nil?
+				q_end_seq=nil #SEQ
+				contig.first_hit.each_hsp_with_index{|hsp,i|
+					q_beg << hsp.q_beg
+					q_end << hsp.q_end
+					s_beg << hsp.s_beg
+					s_end << hsp.s_end
+					#SEQ.................................
+					if i==0
+						seq << contig.seq[0..contig.first_hit.first_hsp.q_end-1] 
+					elsif i+1==n_exones
+						seq << contig.seq[contig.first_hit.hsps[i-1].q_end..contig.length-1]
+					else
+						seq << contig.seq[q_end_seq..hsp.q_end-1]
+					end
+					q_end_seq=hsp.q_end
+					# ...................................
+				}
+				length_model+=contig.length
+				if !reference.nil? #Posicionamiento del primer contig en la referencia
+					last_position_ref,ex=contig.compare(reference)
+					if last_position==-1 || last_position_ref+contig.first_hit.hsp_count-1 > reference.first_hit.hsp_count #Abortar modelado en caso de qun contig no alinee con la referencia o la sobrepase
+					  puts contig.name+' OUT OF RANGE'
+					  out_of_range=TRUE
+					  break
+					end
+				end
+				
+			# OTHER CONTIG 
+			#--------------------------------------------------------	
+			else
+				position_overlap,ex=contig.compare(last_contig)
+
+				#Correccion posicion del contig en base a una referencia
+				if !reference.nil?
+					last_position_ref,position_overlap=position_reference_guided(contig,last_contig,last_position_ref,reference)
+          if last_position_ref==-1 || last_position_ref+contig.first_hit.hsp_count-1 > reference.first_hit.hsp_count
+            out_of_range=TRUE
+            puts contig.name+' OUT OF RANGE'
+            break
+          end
+				end
+	
+				# NOT OVERLAP
+				#..........................
+				if position_overlap==-1 || contig.first_hit.hsp_count==1
+					if contig.first_hit.first_hsp.s_beg-last_contig.first_hit.last_hsp.s_end>1 # Marcar discontinuidad en caso de que el contig no sea correlativo al anterior
+						q_beg << 0
+						q_end << 0
+						s_beg << 0
+						s_end << 0
+						multiple_lengths << length_model
+						length_model=contig.length
+						last=length_model
+						add_length=FALSE
+						seq.last << 'n'*10 #SEQ Indicacion de GAP
+					else
+						last=length_model #Guardamos longitud anterior para poder desplazar las coordenadas del contig correctamente
+						length_model+=contig.length
+					end
+	 
+					q_end_seq=nil #SEQ
+					contig.first_hit.hsps.each_with_index do |hsp,i|
+						add_no=last
+						if !add_length
+							add_no=0
+						end
+						q_beg << hsp.q_beg+add_no # Se acumula a las coordenadas la longitud del modelo
+						q_end << hsp.q_end+add_no
+						s_beg << hsp.s_beg
+						s_end << hsp.s_end
+						#SEQ.................................
+						if i==0
+							cn=contig.seq[0..contig.first_hit.first_hsp.q_end-1]
+							cs="#{cn[0..1].swapcase!}#{cn[2..-1]}"
+							seq << cs					
+						elsif i+1==n_exones
+							seq << contig.seq[contig.first_hit.hsps[i-1].q_end..contig.length-1]						 
+						else
+							seq << contig.seq[q_end_seq..hsp.q_end-1]
+						end
+						q_end_seq=hsp.q_end
+						# ...................................		
+					end
+					
+				# OVERLAP
+				#..........................
+				else
+					if last_position==-1
+						add_last=length_model-last_contig.length
+					end
+					overlap=last_contig.first_hit.hsp_count-position_overlap
+					if last_contig.first_hit.hsp_count ==1
+					  overlap=1
+					end
+          #puts "#{overlap} = #{last_contig.first_hit.hsp_count} - #{position_overlap}"
+  				add=0
+					dif=0
+					if last_score>=score
+						add=last_contig.first_hit.last_hsp.q_end-contig.first_hit.first_hsp.q_end
+						dif=add
+						if overlap>1 #eliminamos ultimo exon de 'last contig' para reemplazar por el segundo de 'contig' q es mas fiable por ser interno
+							add=last_contig.first_hit.hsp_at(last_contig.first_hit.hsp_count-overlap).q_end-contig.first_hit.first_hsp.q_end #Como se dropea el ultimo exon se alinea por el penultimo
+							#puts "hsp:#{contig.first_hit.hsp_count}\toverlap:#{overlap}"
+							dif=contig.first_hit.hsp_at(overlap-1).q_end	
+							q_beg=q_beg.reverse.drop(1).reverse
+							q_end=q_end.reverse.drop(1).reverse
+							s_beg=s_beg.reverse.drop(1).reverse
+							s_end=s_end.reverse.drop(1).reverse
+							seq=seq.reverse.drop(1).reverse #SEQ
+						end
+						if overlap==1
+							overlap=2
+						end
+						(contig.first_hit.hsp_count-(overlap-1)).times do |n| #Añadimos el resto de exones del contig al modelo
+							q_beg << contig.first_hit.hsp_at(n+overlap-1).q_beg+add+add_last
+							q_end << contig.first_hit.hsp_at(n+overlap-1).q_end+add+add_last
+							s_beg << contig.first_hit.hsp_at(n+overlap-1).s_beg
+							s_end << contig.first_hit.hsp_at(n+overlap-1).s_end
+							#SEQ.......................................
+							position_hsp=n+overlap-2
+							if position_hsp <0
+								position_hsp= 0
+							end
+							position_next_hsp=n+overlap-1
+							if position_next_hsp < 0
+								position_next_hsp =0
+							end
+
+							if n==0	
+								cn=contig.seq[contig.first_hit.hsp_at(position_hsp).q_end..contig.first_hit.hsp_at(position_next_hsp).q_end-1]
+								cs=cn[0..1].swapcase!+cn[2..-1] 
+								seq << cs
+							elsif position_next_hsp==contig.first_hit.hsp_count-1
+								seq << contig.seq[contig.first_hit.hsp_at(position_hsp).q_end..contig.length-1]
+							else
+								seq << contig.seq[contig.first_hit.hsp_at(position_hsp).q_end..contig.first_hit.hsp_at(position_next_hsp).q_end-1]
+							end
+							#............................................
+	 					end
+					else
+						hsp_position=last_contig.first_hit.hsp_count-2
+						if hsp_position<0 #para los casos de los contigs q solo poseen un hsp
+							hsp_position=0
+						end
+						add=last_contig.first_hit.hsp_at(hsp_position).q_end
+						dif=last_contig.length-add
+						drop=1
+						correction=0
+						if overlap>1
+							drop=overlap-1
+							correction=1
+							add=last_contig.first_hit.hsp_at(position_overlap).q_end-contig.first_hit.first_hsp.q_end
+							dif=length_model-(add+add_last)
+						end				
+						# Eliminamos exones malos de 'last_contig' (mantenemos el primero del overlap)					
+						q_beg=q_beg.reverse.drop(drop).reverse
+						q_end=q_end.reverse.drop(drop).reverse
+						s_beg=s_beg.reverse.drop(drop).reverse
+						s_end=s_end.reverse.drop(drop).reverse
+						seq=seq.reverse.drop(drop).reverse #SEQ
+	
+						# Añadimos los exones de 'contig' (excepto el primero)
+						(contig.first_hit.hsp_count-correction).times do |n| #Añadimos el resto de exones del contig al modelo
+							q_beg << contig.first_hit.hsp_at(n+correction).q_beg+add+add_last
+							q_end << contig.first_hit.hsp_at(n+correction).q_end+add+add_last
+							s_beg << contig.first_hit.hsp_at(n+correction).s_beg
+							s_end << contig.first_hit.hsp_at(n+correction).s_end
+							#SEQ.............................................................
+							if n+1==(contig.first_hit.hsp_count-correction)
+								n_correction=n+correction-1
+								if n_correction < 0
+									n_correction=0
+								end
+								seq << contig.seq[contig.first_hit.hsp_at(n_correction).q_end..contig.length-1]
+							elsif n==0
+								if n+correction==0
+									cn=contig.seq[0..contig.first_hit.hsp_at(n+correction).q_end-1] # Si n+corr empieza en el primer exon del contig
+								else
+									cn=contig.seq[contig.first_hit.hsp_at(n+correction-1).q_end..contig.first_hit.hsp_at(n+correction).q_end-1]
+								end
+								cs=cn[0..1].swapcase!+cn[2..-1] 
+								seq << cs
+							else
+								seq << contig.seq[contig.first_hit.hsp_at(n+correction-1).q_end..contig.first_hit.hsp_at(n+correction).q_end-1]
+							end
+							#................................................................ 
+						end
+					end
+					length_model+=(contig.length-dif)
+					add_length=TRUE
+					add_last+=add
+				end
+			end
+			last_position=position_overlap
+			last_contig=contig
+			last_score=score
+			lengthy << length_model
+		end
+		if !multiple_lengths.empty?
+			multiple_lengths << length_model
+			length_model=multiple_lengths
+		end
+		
+		model=nil
+		if !out_of_range #Generar modelo si todos los contigs han alineado con la referencia
+      model=void_contig(contigs.first.first_hit.name+'_model',length_model,contigs.first.first_hit.s_length,q_beg,q_end,s_beg,s_end,'contig','gene','exon')
+      #Merge contigs under sequence reference
+      model_length=nil
+      if model.class.to_s=='Array'
+        add=0
+        model.each_with_index do |contig,i|
+          contig.modified_coordenates(add)
+          add+=contig.length
+          if i<model.length-1
+            add+=10
+          end
+        end
+        model_length=add+model.last.length
+      end
+    
+      model_n_exones=seq.length
+    	final_seq=seq.join
+  else #No generar modelo si al menos un contig no alinea contra la referencia
+       model_length=nil
+       final_seq=nil
+    end
+
+		return model, model_length, final_seq
+	end
+	
+	def void_contig(contig_name,contig_length,s_length,q_beg,q_end,s_beg,s_end,contig_type,hit_type,hsp_type,single=FALSE) #Genera un objeto contig con los datos proporcionados
+		contigs=[]
+		is_contig=1
+		contig=nil
+		n=0
+		q_beg.each_with_index do |item,ind|
+			if item>0 ||single
+				if contig==nil
+					if contig_length.class.to_s=='Array'
+						length=contig_length[n]
+						name="#{contig_name}_#{n}"
+					else
+						length=contig_length
+						name=contig_name
+					end
+					contig=Contig.new(name)
+					contig.length=length
+					contig.type=contig_type
+					hit_v=contig.add_hit(contig_name,s_length,1,:prot)
+					hit_v.type=hit_type
+				end
+				hsp_v=contig.first_hit.add_hsp(q_beg[ind], q_end[ind], s_beg[ind], s_end[ind], 0, 0, 0, 0)
+				hsp_v.type=hsp_type
+			end
+			if item==0 && contig!=nil && !single||q_beg.length-1==ind
+				if single ||!q_beg.include?(0)
+					contigs=contig
+				else
+					contigs << contig
+				end
+				n+=1
+				contig=nil
+			end
+		end
+		return contigs
+	end
+
+	def position_reference_guided(contig,last_contig,last_position_ref,reference)# Si no existe overlap devuelve -1
+		position_ref,ex=contig.compare(reference)
+		if !last_position_ref.nil?
+			if position_ref<=last_position_ref+(last_contig.first_hit.hsp_count-1) #Overlap
+				position_overlap=(last_position_ref-position_ref).abs
+			else #No overlap
+				position_overlap=-1
+			end
+		end
+		return position_ref,position_overlap
+	end
+	
+	def array_contigs_to_contig(array_contigs)
+	  contig=Contig.new(array_contigs.first.name)
+	  array_contigs.each do |cn|
+	      contig.transfer_contig_hits(cn)
+	  end
+	  contig.length=array_contigs.last.length
+	  return contig
+	end
+	
+	def gene_error(e, gene_name, file_error, cluster, model) #e is a ruby exception object
+    puts gene_name+' ERROR'
+    file_error.puts "\n"+gene_name+"\n.............................."
+    file_error.puts e.message
+    e.backtrace.each do |line|
+      file_error.puts line
+    end
+    file_error.puts ',,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,'
+    cluster.each do |contig|
+      file_error.puts contig.name
+      #puts contig.name
+      #contig.indices
+    end
+    file_error.puts '----------------------------------------------------------------------------------------'
+	end
+	
+	def overlap_test(model,output=TRUE)
+    perc_overlap=0
+    overlap=model.overlap
+    total=0
+    if !overlap.empty?
+      if output
+        print 'WARNING: overlap/s '
+      end
+      overlap.each do |length_overlap|
+        if output
+          print (length_overlap*-3).to_s+', '
+        end
+        total+=length_overlap
+      end
+      perc_overlap=(total*-100.0/model.first_hit.s_length).round(2)
+      if output
+        puts 'nt. % Total overlap '+perc_overlap.to_s
+      end
+    end
+    return perc_overlap    
+	end
+	
+	def recover_test(model,output=TRUE)
+		recovered=0
+		model.exones_s.each do |exon|
+			recovered+=exon
+		end		
+    recovered=(recovered*100.0/model.first_hit.s_length).round(2)
+    if output
+		  puts "Recovered\t"+model.first_hit.name+"\t#{recovered}"
+		end
+		return recovered
+	end
+
+  def web_header(web, path)
+    file_web=nil
+    if web
+      file_web=File.open(path,'w')
+      html_header(file_web,'Gene index')
+      html_table_header(file_web,1,['Gene model name', 'Protein length', 'Num exon', '% recovered protein', '% overlapping sequence', 'Fragmentation'])
+    end
+    return file_web
+  end
+  
+  def web_body(file_web)
+    if !file_web.nil?
+      html_table_footer(file_web)
+      html_footer(file_web)
+      file_web.close
+    end
+  end
+  
+  def write_model_fasta(sequences_hash, path)
+    model_file=File.open(path,'w')
+    sequences_hash.each do |model|
+      model_file.puts '>'+model[0]+"_model\n"+model[1]
+    end
+    model_file.close
+  end
+  
+  def write_gbrowse_gff(gff_dataset_model, gff_dataset, path, name)
+    gff_model=ReportGff.new(gff_dataset_model,path,'s')
+    gff_model.create('a')
+    gff=ReportGff.new(gff_dataset,path,'s')
+    gff.create('a',name)
+  end
+  
+  def format_model(model)
+    if model.n_hits?>1
+      model.each_hit_with_index{|hit,i|
+        hit.name=hit.name+"_gene_#{i}"
+      }
+    else
+      model.first_hit.name=model.first_hit.name+'_gene'
+    end
+  end
+  
+  def correct_model(model, length_model, gff_dataset, sequences_hash)
+    correct_add_Ns=0
+    if model.class.to_s=='Array'
+      model=array_contigs_to_contig(model)
+      model.name=model.name.gsub('_0','')
+      model.length=length_model
+    end
+    
+    correct_add_Ns=gff_dataset.correct_left_side_contigs(model)
+    model.modified_coordenates(correct_add_Ns)
+    model.length+=correct_add_Ns
+    gff_dataset.align_contigs(model)
+  
+  	 #Corregir secuencia para que alinee con las features generadas
+  	 if correct_add_Ns>0
+      sequences_hash[model.name.gsub('_model','')]='n'*correct_add_Ns+sequences_hash[model.name.gsub('_model','')]
+  	 end
+    	
+	  return model
+  end
+  	
+end