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