protk 1.2.6.pre5 → 1.3.0.pre1

data/lib/protk/gapped_aligner.rb

@@ -1,264 +0,0 @@
-require 'bio'
-require 'matrix'
-
-class PeptideFragment
-	attr_accessor :start
-	attr_accessor :end
-	attr_accessor :seq
-end
-
-class PeptideToGeneAlignment
-	attr_accessor :gene_seq
-	attr_accessor :pep_seq
-	attr_accessor :trace
-
-	def initialize(gene,peptide,trace)
-		@gene_seq = gene
-		@pep_seq = peptide
-		@trace = trace
-	end
-
-	def inspect
-		descr = "#{@gene_seq}\n"
-
-		pep_triples=""
-		@pep_seq.each_char { |c| pep_triples<<c;pep_triples<<c;pep_triples<<c }
-		
-		# gene_seq_triples=""
-		# Bio::Sequence::NA.new(@gene_seq).translate.each_char do |c| 
-		# 	gene_seq_triples<<c;gene_seq_triples<<c;gene_seq_triples<<c 
-		# end
-
-		# descr << "#{gene_seq_triples}\n"
-		
-		pepi=0
-		@trace.each_with_index do |move, i|  
-			if move==1
-				descr<<"-"
-			elsif move==0
-				descr<<"#{pep_triples[pepi]}"
-				pepi+=1
-			end
-		end
-		descr<<"\n"
-		puts descr
-	end
-
-	def fragments
-		frags=[]
-		in_fragment=false
-		@trace.each_with_index do |move,i|
-			if move==0
-				frags << [i,0] unless in_fragment #Start a fragment
-				in_fragment=true	
-			else
-				frags.last[1]=i-1 if in_fragment #End a fragment
-				in_fragment=false
-			end					
-		end
-		if frags.last[1]==0
-			frags.last[1]=@trace.length-1
-		end
-		frags
-	end
-
-	def gaps
-		gps=[]
-		in_start_end=true
-		in_gap=false
-		@trace.each_with_index do |move, i| 
-			if move==0
-				in_start_end=false
-				if in_gap #Ending a gap
-					gps.last[1]=i
-				end
-				in_gap=false
-			else
-				if !in_start_end && !in_gap #Starting a gap
-					in_gap=true
-					gps<<[i,0]
-				end
-			end				
-		end
-		#Remove gaps that have zero length (Trailing)
-		gps=gps.collect do |gp| 
-			rv=gp
-			if gp[1]==0
-				rv=nil
-			end		
-			rv
-		end
-		gps.compact!
-		gps
-	end
-
-end
-
-# Uses a dynamic programming algorithm (Smith-Waterman like) to align a peptide sequence to a nucleotide.
-# This aligner assumes you are doing protogenomics and just want to assume that
-#    (a) The entire peptide sequence matches (with gaps) to the DNA sequence
-#
-class GappedAligner
-
-	def initialize
-		@big_penalty = -1000000000
-		@gap_open_penalty = -10000
-		@gap_extend_penalty = -1
-		@end_gap_penalty = 0
-		@match_bonus = 400
-
-		@match_move=0
-		@aadel_move=-1
-		@nadel_move=1
-		@triplet_offsets = [[0,-2,-1],[-1,0,-2],[-2,-1,0]]
-	end
-
-	def aa_deletion()
-		return @big_penalty
-	end
-
-	def score_na_deletion(move_type)
-		if move_type==@nadel_move
-			return @gap_extend_penalty
-		end
-		return @gap_open_penalty
-	end
-
-	def score_match(aa,na)
-		if aa==na
-			return @match_bonus		
-		end
-		return @big_penalty
-	end
-
-	def traceback(from_row,from_col,dpmoves)
-		last_move = dpmoves[from_row][from_col]
-		last_row = from_row-1
-		last_col = from_col-1
-		if last_move==@aadel_move
-			last_col+=1
-		elsif last_move==@nadel_move			
-			last_row+=1
-		end
-
-		if last_col==0 && last_row==0
-			return [last_move]
-		else
-			throw "Beyond end of array" if last_col<0 || last_row <0
-
-			return traceback(last_row,last_col,dpmoves).push(last_move)
-		end
-	end
-
-	def next_frame(previous_frame)
-		(previous_frame+1) % 3
-	end
-
-	def translate_na_at(j,frame,gene_seq)
-		rm = j % 3 
-		start_pos=j+@triplet_offsets[rm][frame]
-		if start_pos < 0
-			return '-'
-		else
-			return gene_seq[start_pos,3].translate
-		end
-	end
-
-	def save_matrix(dpmatrix,pep_triples,gene_seq,name)
-		matfile=File.open("#{name}.csv", "w+")
-		matfile.write(",,")
-		gene_seq.each_char { |na| matfile.write("#{na},")  }
-		matfile.write("\n")
-		dpmatrix.each_with_index { |row,ri|  
-			if ri>0
-				matfile.write("#{pep_triples[ri-1]},")
-			else
-				matfile.write(",")
-			end
-			row.each { |col|  
-				matfile.write("#{col},")
-			}
-			matfile.write("\n")
-		}
-		matfile.close()
-	end
-
-	def calculate_dp(pep_seq,gene_seq)
-		gene_seq = Bio::Sequence::NA.new(gene_seq)
-		nrow = pep_seq.length*3+1
-		ncol = gene_seq.length+1
-
-		throw "Peptide sequence is longer than gene" if nrow > ncol
-
-		pep_triples=""
-		pep_seq.each_char { |c| pep_triples<<c;pep_triples<<c;pep_triples<<c }
-
-		dpmoves=Matrix.build(nrow,ncol) {|r,c| 0 }.to_a
-		dpmatrix=Matrix.build(nrow,ncol) { |r,c| 0 }.to_a
-		dpframes=Matrix.build(nrow,ncol) { |r,c| 0 }.to_a
-		# before_gap_positions = Matrix.build(nrow,ncol) { |r,c| 0 }.to_a
-
-		# Boundary conditions
-		(0..(nrow-1)).each { |i| 
-			dpmatrix[i][0] = aa_deletion*i 
-			dpmoves[i][0] = @aadel_move
-		}
-		(0..(ncol-1)).each { |j| 
-			dpmatrix[0][j] = @end_gap_penalty*j 
-			dpmoves[0][j] = @nadel_move
-			dpframes[0][j] = j % 3
-		}
-		dpmoves[0][0]=0
-		dpframes[0][0]=0
-
-		(1..(nrow-1)).each do |i|
-			(1..(ncol-1)).each do |j|
-				aa = pep_triples[i-1]
-
-				translated_na = translate_na_at(j-1,dpframes[i-1][j-1],gene_seq)
-
-				match = score_match(aa,translated_na) + dpmatrix[i-1][j-1]
-
-				nadel = score_na_deletion(dpmoves[i][j-1]) + dpmatrix[i][j-1]
-
-				# if (translated_na=="R") && (pep_seq=="FR") && (aa == "R")
-					# require 'debugger';debugger					
-				# end
-
-				if match >= nadel
-					dpmatrix[i][j] = match					
-					dpmoves[i][j] = @match_move
-					dpframes[i][j] = dpframes[i-1][j-1]
-				else
-					dpmatrix[i][j] = nadel
-					dpmoves[i][j] = @nadel_move
-					dpframes[i][j] = next_frame(dpframes[i][j-1])
-				end
-
-			end
-		end
-
-		# Find best end-point
-		end_score = dpmatrix[nrow-1].max
-		end_j = dpmatrix[nrow-1].index(end_score)
-
-		save_matrix(dpmatrix,pep_triples,gene_seq,"dpmatrix")
-		save_matrix(dpmoves,pep_triples,gene_seq,"moves")
-		save_matrix(dpframes,pep_triples,gene_seq,"frames")
-#		require 'debugger';debugger
-
-		traceback(nrow-1,end_j,dpmoves)
-	end
-
-
-	def align pep_seq, gene_seq
-
-		trace = calculate_dp(pep_seq,gene_seq)
-		alignment = PeptideToGeneAlignment.new(gene_seq,pep_seq,trace)
-		# puts alignment
-		# require 'debugger';debugger
-
-		return alignment
-	end
-
-end