Class: Bio::DB::Pileup

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/db/pileup.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(pile_up_line) ⇒ Pileup

creates the Pileup object

pile_up_line = "seq2\t151\tG\tG\t36\t0\t99\t12\t...........A\t:9<;;7=<<<<<"
pile = Bio::DB::Pileup.new(pile_up_line)



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# File 'lib/bio/db/pileup.rb', line 35

def initialize(pile_up_line)
  cols = pile_up_line.split(/\t/)
  if cols.length == 6 ##should only be able to get 6 lines from mpileup
    @ref_name, @pos, @ref_base, @coverage, @read_bases, @read_quals = cols
  elsif (10..13).include?(cols.length) ##incase anyone tries to use deprecated pileup with -c flag we get upto 13 cols...
    @ref_name, @pos, @ref_base, @consensus, @consensus_quality, @snp_quality, @rms_mapq, @coverage, @read_bases, @read_quals, @ar1, @ar2, @ar3 = cols
    @consensus_quality = @consensus_quality.to_f
    @snp_quality = @snp_quality.to_f
    @rms_mapq = @rms_mapq.to_f
  else
    #raise RuntimeError, "parsing line '#{pile_up_line.chomp}' failed"
  end
    
  @pos = @pos.to_i
  @coverage = @coverage.to_f
  @ref_count = nil
  @non_ref_count_hash = nil 
  @non_ref_count = nil
end

Instance Attribute Details

#ar1 ⇒ Object

Returns the value of attribute ar1.



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# File 'lib/bio/db/pileup.rb', line 30

def ar1
  @ar1
end

#ar2 ⇒ Object

Returns the value of attribute ar2.



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# File 'lib/bio/db/pileup.rb', line 30

def ar2
  @ar2
end

#ar3 ⇒ Object

Returns the value of attribute ar3.



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# File 'lib/bio/db/pileup.rb', line 30

def ar3
  @ar3
end

#consensus ⇒ Object

returns the consensus (most frequent) base from the pileup, if there are equally represented bases returns a string containing all equally represented bases in alphabetical order



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# File 'lib/bio/db/pileup.rb', line 81

def consensus
  @consensus
end

#consensus_quality ⇒ Object

Returns the value of attribute consensus_quality.



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# File 'lib/bio/db/pileup.rb', line 30

def consensus_quality
  @consensus_quality
end

#coverage ⇒ Object

Returns the value of attribute coverage.



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# File 'lib/bio/db/pileup.rb', line 30

def coverage
  @coverage
end

#pos ⇒ Object

Returns the value of attribute pos.



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# File 'lib/bio/db/pileup.rb', line 30

def pos
  @pos
end

#read_bases ⇒ Object

Returns the value of attribute read_bases.



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# File 'lib/bio/db/pileup.rb', line 30

def read_bases
  @read_bases
end

#read_quals ⇒ Object

Returns the value of attribute read_quals.



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# File 'lib/bio/db/pileup.rb', line 30

def read_quals
  @read_quals
end

#ref_base ⇒ Object

Returns the value of attribute ref_base.



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# File 'lib/bio/db/pileup.rb', line 30

def ref_base
  @ref_base
end

#ref_name ⇒ Object

Returns the value of attribute ref_name.



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# File 'lib/bio/db/pileup.rb', line 30

def ref_name
  @ref_name
end

#rms_mapq ⇒ Object

Returns the value of attribute rms_mapq.



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# File 'lib/bio/db/pileup.rb', line 30

def rms_mapq
  @rms_mapq
end

#snp_quality ⇒ Object

Returns the value of attribute snp_quality.



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# File 'lib/bio/db/pileup.rb', line 30

def snp_quality
  @snp_quality
end

Instance Method Details

#non_ref_count ⇒ Object

returns the total non-reference bases in the reads at this position



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# File 'lib/bio/db/pileup.rb', line 65

def non_ref_count
  if @non_ref_count.nil?
    @non_ref_count = @read_bases.count("ATGCatgc").to_f
  end
  @non_ref_count
end

#non_refs ⇒ Object

Calculate the total count of each non-reference nucleotide and return a hash of all 4 nt counts, returns a hash

pile.non_refs #{:A => 1, :C => 0, :T => 0, :G => 0}



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# File 'lib/bio/db/pileup.rb', line 57

def non_refs
  if @non_ref_count_hash.nil?
     @non_ref_count_hash = {:A => self.read_bases.count("Aa"), :C => self.read_bases.count("Cc"), :G => self.read_bases.count("Gg"), :T => self.read_bases.count("Tt")}
  end
    @non_ref_count_hash
end

#ref_count ⇒ Object

returns the count of reference-bases in the reads at this position



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# File 'lib/bio/db/pileup.rb', line 73

def ref_count
  if @ref_count.nil?
    @ref_count = self.read_bases.count(".,")
  end
  @ref_count
end