Class: PeptideToGeneAlignment

Inherits:
Object
  • Object
show all
Defined in:
lib/protk/gapped_aligner.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(gene, peptide, trace) ⇒ PeptideToGeneAlignment

Returns a new instance of PeptideToGeneAlignment.



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# File 'lib/protk/gapped_aligner.rb', line 15

def initialize(gene,peptide,trace)
	@gene_seq = gene
	@pep_seq = peptide
	@trace = trace
end

Instance Attribute Details

#gene_seq ⇒ Object

Returns the value of attribute gene_seq.



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# File 'lib/protk/gapped_aligner.rb', line 11

def gene_seq
  @gene_seq
end

#pep_seq ⇒ Object

Returns the value of attribute pep_seq.



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# File 'lib/protk/gapped_aligner.rb', line 12

def pep_seq
  @pep_seq
end

#trace ⇒ Object

Returns the value of attribute trace.



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# File 'lib/protk/gapped_aligner.rb', line 13

def trace
  @trace
end

Instance Method Details

#fragments ⇒ Object 



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# File 'lib/protk/gapped_aligner.rb', line 47

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

#gaps ⇒ Object 



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# File 'lib/protk/gapped_aligner.rb', line 65

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

#inspect ⇒ Object 



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# File 'lib/protk/gapped_aligner.rb', line 21

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