Class: UneLosHit

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(full_hit, query_fasta) ⇒ UneLosHit

Returns a new instance of UneLosHit.



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

def initialize(full_hit, query_fasta)
	#puts 'BEG ___________________'
	#full_hit.map{|hsp| puts hsp.inspect}
	mismas_ids_array, query_fasta = hits_misma_id(full_hit, query_fasta)
	#puts '..................'
	@mismas_ids_array = mismas_ids_array
	@msgs = []
	@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.shift # We take first hsp like reference for unigene reconstruction
		#puts @output_seq.length
		#puts "\e[32m#{@final_hit.inspect}\e[0m"
		mismas_ids_array.each do |hit|
			#puts '.....', "\e[31m#{hit.inspect}\e[0m"
			##if @final_hit.q_frame == hit.q_frame #Same frame
			##	puts "\e[33mSame Frame\e[0m"
			##	same_frame_hits_query(hit)
			if  overlapping_hits?(hit) #Diff frame
				if @msgs.empty?
					@msgs << ['OverlapHit', @final_hit.q_end + 1, hit.q_beg + 1]
				else
					@msgs << ['AndOverlapHit', @final_hit.q_end + 1, hit.q_beg + 1]
				end
				#puts "\e[33mOverlapped hits\e[0m"
				overlapped_hits_query(hit)			
			elsif  separated_hits?(hit) #Diff frame
				if @msgs.empty?
					@msgs << ['SeparatedHit', @final_hit.q_end + 1, hit.q_beg + 1]
      				else
					@msgs << ['AndSeparatedHit', @final_hit.q_end + 1, hit.q_beg + 1]
				end
				#puts "\e[33mSeparated hits\e[0m"
				separated_hits(hit) #Diff frame
			end
		#puts @output_seq.length
		#puts  '.....'
		#puts "\e[32m#{@final_hit.inspect}\e[0m"
		end
	else
		@final_hit = mismas_ids_array.shift			
	end
	#puts 'END ___________________'
	#puts @final_hit.inspect
end

Instance Attribute Details

#final_hit ⇒ Object (readonly)

Returns the value of attribute final_hit.



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

def q_index_start
  @q_index_start
end

Instance Method Details

#ajust_nt(nt) ⇒ Object

Returns the number of nt necessary for keep the ORF (or nt becomes multiple of 3)



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# File 'lib/full_lengther_next/une_los_hit.rb', line 196

def ajust_nt(nt) # Returns the number of nt necessary for keep the ORF (or nt becomes multiple of 3) 
	add=0
	if nt % 3 == 1
		add = 2
	elsif nt % 3 == 2
		add = 1
	end
	return add
end

#hits_misma_id(full_hit, 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/une_los_hit.rb', line 156

def hits_misma_id(full_hit, query_fasta_ori)		
	# Se les hace la reverso complementaria si es necesario
	misma_id = []
	query_fasta = query_fasta_ori.dup
	#frame_ori = q.hits.first.q_frame

	full_hit.each do |h|
		if h.acc == full_hit.first.acc
			# comprobar si los frames tienen el mismo sentido
			#if frame_ori < 0 && h.q_frame > 0 || frame_ori > 0 && h.q_frame < 0
				if h.q_frame < 0 # si la secuencia esta al reves le damos la vuelta
					query_fasta = reverse_seq(query_fasta_ori, h)
					h.reversed = true
				end
				misma_id << h
			#end
		end
	end

	return misma_id, query_fasta
end

#overlapped_hits(hit) ⇒ Object

Colapsa cuando hay hsps en diferentes partes de la query pero son lo mismo en el subject con lo cual los eliminamos antes



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# File 'lib/full_lengther_next/une_los_hit.rb', line 103

def overlapped_hits(hit) #Colapsa cuando hay hsps en diferentes partes de la query pero son lo mismo en el subject con lo cual los eliminamos antes
	overlapped_aas = @final_hit.s_end - hit.s_beg + 1
	overlapped_nts = @final_hit.q_end - hit.q_beg + 1
	align_len_final_hit = @final_hit.q_seq.length
	hit_gaps_query = @final_hit.q_seq[align_len_final_hit-overlapped_aas..align_len_final_hit].count('-')
	hit_gaps_subject = @final_hit.s_seq[0..align_len_final_hit].count('-')
	total_gaps = (hit_gaps_query - hit_gaps_subject).abs # Gaps añaden aa q no existen, x lo q han de descontarse
	nt_discount = (overlapped_aas ) * 3

	absolute_overlap = 1
	if nt_discount < 0 #Not overlap on subject
           overlapped_aas = overlapped_aas.abs
		absolute_overlap = 0 #Don't cut q_seq and s_seq, because there is query overlap but there isn't subject overlap
		nt_discount =  @final_hit.q_end - hit.q_beg + 1
		nt_discount += ajust_nt(nt_discount)
	end
	add_nt = overlapped_nts + ajust_nt(hit.q_frame-1)
	@output_seq = @output_seq[0..@final_hit.q_end-overlapped_nts] + 'n' * add_nt + @output_seq[@final_hit.q_end+1.. @output_seq.length-1]

	#q_seq and s_seq are aa sequences
	final_hit_upper_bound = @final_hit.q_seq.length - 1 - overlapped_aas * absolute_overlap
	@final_hit.q_seq = @final_hit.q_seq[0..final_hit_upper_bound] + 'x' * overlapped_aas + hit.q_seq[overlapped_aas * absolute_overlap .. hit.q_seq.length-1]
	@final_hit.s_seq = @final_hit.s_seq[0..final_hit_upper_bound] + 'x' * overlapped_aas + hit.s_seq[overlapped_aas * absolute_overlap .. hit.s_seq.length-1]

	@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
	@final_hit.align_len = @final_hit.s_end - @final_hit.s_beg+1		
end

#overlapped_hits_query(hit) ⇒ Object 



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# File 'lib/full_lengther_next/une_los_hit.rb', line 64

def overlapped_hits_query(hit)
	overlapped_nts = @final_hit.q_end - hit.q_beg + 1
	add_nt = ajust_nt(hit.q_frame-1) # Fix frame-shift
	@output_seq = @output_seq[0..@final_hit.q_end-overlapped_nts] + 'n' * (overlapped_nts + add_nt) + @output_seq[@final_hit.q_end+1.. @output_seq.length-1]

	@final_hit.q_seq = @output_seq[@final_hit.q_beg..hit.q_end+add_nt].translate
	@final_hit.q_end = hit.q_end + add_nt
	
	@final_hit.s_beg = [@final_hit.s_beg, hit.s_beg].min
	@final_hit.s_end = [@final_hit.s_end, hit.s_end].max
	@final_hit.align_len = @final_hit.s_end - @final_hit.s_beg+1
	@final_hit.q_len = @output_seq.length
end

#overlapping_hits?(hit) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/full_lengther_next/une_los_hit.rb', line 178

def overlapping_hits?(hit)
	overlap = false
	if @final_hit.q_end >= hit.q_beg && @final_hit.q_end < hit.q_end && @final_hit.q_end < hit.q_end
		overlap = true
	end
	return overlap
end

#same_frame_hits(hit) ⇒ Object 



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# File 'lib/full_lengther_next/une_los_hit.rb', line 92

def same_frame_hits(hit)
	add = (hit.s_beg - @final_hit.s_end) + 1
	nt_add = add *3
	@final_hit.q_seq = @final_hit.q_seq + 'x' * add + hit.q_seq
	@final_hit.s_seq = @final_hit.s_seq + 'x' * add + hit.s_seq
	@output_seq = @output_seq[0..@final_hit.q_end-nt_add] + 'n'*nt_add  + @output_seq[hit.q_beg+1..@output_seq.length-1]
	@final_hit.q_end = hit.q_end
	@final_hit.s_end = hit.s_end
	@final_hit.align_len = hit.s_end - @final_hit.s_beg + 1
end

#same_frame_hits_query(hit) ⇒ Object 



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# File 'lib/full_lengther_next/une_los_hit.rb', line 56

def same_frame_hits_query(hit)
	@final_hit.q_seq = @output_seq[@final_hit.q_beg..@final_hit.q_end].translate
	@final_hit.q_end = hit.q_end
	@final_hit.s_end = hit.s_end
	@final_hit.align_len = hit.s_end - @final_hit.s_beg + 1
end

#separated_hits(hit) ⇒ Object 



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# File 'lib/full_lengther_next/une_los_hit.rb', line 134

def separated_hits(hit)			
	number_x = hit.q_beg - @final_hit.q_end - 1
	number_x += ajust_nt(number_x)	

	num_x = ''
	num_x_aa = ''
	if number_x > 0
		num_x = 'n'*number_x
		num_x_aa = 'x'*(number_x/3)
	end
	@output_seq = @output_seq[0..@final_hit.q_end-1] + num_x + @output_seq[hit.q_beg-1..@output_seq.length-1]
       @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]

	@final_hit.q_end = hit.q_end
	@final_hit.s_end = hit.s_end
	@final_hit.align_len = @final_hit.s_end - @final_hit.s_beg+1	
end

#separated_hits?(hit) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/full_lengther_next/une_los_hit.rb', line 186

def separated_hits?(hit)
	separated=false
	if @final_hit.q_end < hit.q_beg && hit.q_end > @final_hit.q_end
		separated = true
	end
	return separated
end

#separated_hits_query(hit) ⇒ Object 



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# File 'lib/full_lengther_next/une_los_hit.rb', line 79

def separated_hits_query(hit)			
	separated_nts = hit.q_beg - @final_hit.q_end + 1
	add_nt = ajust_nt(separated_nts) # Fix frame-shift

	@output_seq = @output_seq[0..@final_hit.q_end - separated_nts] + 'n' * (separated_nts + add_nt) + @output_seq[@final_hit.q_end+1..@output_seq.length-1]
	@final_hit.q_seq = @output_seq[@final_hit.q_beg..hit.q_end+add_nt].translate

	@final_hit.q_end = hit.q_end + add_nt
	@final_hit.s_end = hit.s_end
	@final_hit.align_len = @final_hit.s_end - @final_hit.s_beg+1
	@final_hit.q_len = @output_seq.length
end