Class: Bio::Util::MrnaModel

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/utils/bio-synreport.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(chr, id, strand, cds_arr, seq_arr) ⇒ MrnaModel

Returns a new instance of MrnaModel.



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# File 'lib/bio/utils/bio-synreport.rb', line 11

def initialize(chr, id, strand, cds_arr, seq_arr)
  @seqname, @gff_id, @strand, @cds, @sequences = chr, id, strand, cds_arr, seq_arr
end

Instance Attribute Details

#cds ⇒ Object

Returns the value of attribute cds.



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# File 'lib/bio/utils/bio-synreport.rb', line 9

def cds
  @cds
end

#gff_id ⇒ Object

Returns the value of attribute gff_id.



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# File 'lib/bio/utils/bio-synreport.rb', line 9

def gff_id
  @gff_id
end

#seqname ⇒ Object

Returns the value of attribute seqname.



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# File 'lib/bio/utils/bio-synreport.rb', line 9

def seqname
  @seqname
end

#sequences ⇒ Object

Returns the value of attribute sequences.



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# File 'lib/bio/utils/bio-synreport.rb', line 9

def sequences
  @sequences
end

#strand ⇒ Object

Returns the value of attribute strand.



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# File 'lib/bio/utils/bio-synreport.rb', line 9

def strand
  @strand
end

Instance Method Details

#includes?(seq, point) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bio/utils/bio-synreport.rb', line 15

def includes?(seq, point)
  @cds.each {|start, stop| return true if @seqname == seq and point.to_i >= start and point.to_i <= stop}
  false
end

#seq ⇒ Object 



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# File 'lib/bio/utils/bio-synreport.rb', line 20

def seq
  @sequences.join
end

#substitution_info(chr, point, alt) ⇒ Object 



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# File 'lib/bio/utils/bio-synreport.rb', line 24

def substitution_info(chr,point,alt)
  cds_start = @cds.first.first
  running_total = 0
  @cds.each do |start,stop|
    if point.to_i >= start and point.to_i <= stop
      offset = case @strand
      when "+"
        #offset = 
        (point.to_i - start) + running_total
      when "-"
        (stop - point.to_i) + running_total 
      end  #offset = how far into cds SNP is
      codon_number = offset / 3
      position_in_codon = offset % 3
      #pp [offset, codon_number, position_in_codon] 
      codon_array = []; Bio::Sequence::NA.new(self.seq).window_search(3,3) {|b| codon_array << b}
      codon = codon_array[codon_number]
      nt = codon[position_in_codon]
      new_codon = codon.dup
      new_codon[position_in_codon] = alt.downcase
      #pp [codon, position_in_codon, nt, new_codon]
      a = Bio::Sequence::NA.new(codon).translate.codes.first
      b =  Bio::Sequence::NA.new(new_codon).translate.codes.first
      sub_type = a == b ? "SYN" : "NON_SYN"
      return {:id => @gff_id, 
              :chr => @seqname, 
              :strand => @strand, 
              :position => point,
              :original_codon => codon, 
              :original_residue => a || 'stop', 
              :mutant_codon => new_codon, 
              :mutant_residue =>b || 'stop', 
              :position_in_codon => position_in_codon + 1, 
              :substitution_type => sub_type
              }
    end
    running_total += (stop - start)
    running_total += 1 if @strand == '-' #how far we are into the cds
  end
end