Class: Cheripic::Contig

Inherits:
Object
  • Object
show all
Defined in:
lib/cheripic/contig.rb

Overview

A contig object from assembly that stores positions of homozygous, heterozygous and hemi-variants

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(fasta) ⇒ Contig

creates a Contig object using fasta entry

Parameters:

  • fasta (Bio::FastaFormat) —

    an individual fasta entry from input assembly file



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# File 'lib/cheripic/contig.rb', line 30

def initialize (fasta)
  @id = fasta.entry_id
  @length = fasta.length
  @hm_pos = {}
  @ht_pos = {}
  @hemi_pos = {}
  @mean_depth = nil
  @sd_depth = nil
end

Instance Attribute Details

#hemi_pos ⇒ Hash

Returns a hash of hemi-variant positions as keys and allele frequency as values.

Returns:

  • (Hash) —

    a hash of hemi-variant positions as keys and allele frequency as values



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# File 'lib/cheripic/contig.rb', line 23

class Contig

  attr_accessor :hm_pos, :ht_pos, :hemi_pos, :mean_depth, :sd_depth
  attr_reader :id, :length

  # creates a Contig object using fasta entry
  # @param fasta [Bio::FastaFormat] an individual fasta entry from input assembly file
  def initialize (fasta)
    @id = fasta.entry_id
    @length = fasta.length
    @hm_pos = {}
    @ht_pos = {}
    @hemi_pos = {}
    @mean_depth = nil
    @sd_depth = nil
  end

  # Number of homozygous variants identified in the contig
  # @return [Integer]
  def hm_num
    self.hm_pos.length
  end

  # Number of heterozygous variants identified in the contig
  # @return [Integer]
  def ht_num
    self.ht_pos.length
  end

  # Homozygosity enrichment score calculated using
  # hm_num and ht_num of the contig object
  # @return [Float]
  def hme_score
    hmes_adjust = Options.hmes_adjust
    if self.hm_num == 0 and self.ht_num == 0
      0.0
    else
      (self.hm_num + hmes_adjust) / (self.ht_num + hmes_adjust)
    end
  end

  # Number of hemi-variants identified in the contig
  # @return [Integer]
  def hemi_num
    self.hemi_pos.length
  end

  # Mean of bulk frequency ratios (bfr) calculated using
  # bfr values all hemi_pos of the contig
  # @return [Float]
  def bfr_score
    if self.hemi_pos.values.empty?
      0.0
    else
      geom_mean(self.hemi_pos.values)
    end
  end

  # Calculates mean of an array of numbers
  # @param array [Array] an array of bfr values from hemi_snp
  # @return [Float] mean value as float
  def geom_mean(array)
    return array[0].to_f if array.length == 1
    array.reduce(:+) / array.size.to_f
    # sum = 0.0
    # array.each{ |v| sum += Math.log(v.to_f) }
    # sum /= array.size
    # Math.exp sum
  end

end

#hm_pos ⇒ Hash

Returns a hash of homozygous variant positions as keys and allele frequency as values.

Returns:

  • (Hash) —

    a hash of homozygous variant positions as keys and allele frequency as values



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# File 'lib/cheripic/contig.rb', line 23

class Contig

  attr_accessor :hm_pos, :ht_pos, :hemi_pos, :mean_depth, :sd_depth
  attr_reader :id, :length

  # creates a Contig object using fasta entry
  # @param fasta [Bio::FastaFormat] an individual fasta entry from input assembly file
  def initialize (fasta)
    @id = fasta.entry_id
    @length = fasta.length
    @hm_pos = {}
    @ht_pos = {}
    @hemi_pos = {}
    @mean_depth = nil
    @sd_depth = nil
  end

  # Number of homozygous variants identified in the contig
  # @return [Integer]
  def hm_num
    self.hm_pos.length
  end

  # Number of heterozygous variants identified in the contig
  # @return [Integer]
  def ht_num
    self.ht_pos.length
  end

  # Homozygosity enrichment score calculated using
  # hm_num and ht_num of the contig object
  # @return [Float]
  def hme_score
    hmes_adjust = Options.hmes_adjust
    if self.hm_num == 0 and self.ht_num == 0
      0.0
    else
      (self.hm_num + hmes_adjust) / (self.ht_num + hmes_adjust)
    end
  end

  # Number of hemi-variants identified in the contig
  # @return [Integer]
  def hemi_num
    self.hemi_pos.length
  end

  # Mean of bulk frequency ratios (bfr) calculated using
  # bfr values all hemi_pos of the contig
  # @return [Float]
  def bfr_score
    if self.hemi_pos.values.empty?
      0.0
    else
      geom_mean(self.hemi_pos.values)
    end
  end

  # Calculates mean of an array of numbers
  # @param array [Array] an array of bfr values from hemi_snp
  # @return [Float] mean value as float
  def geom_mean(array)
    return array[0].to_f if array.length == 1
    array.reduce(:+) / array.size.to_f
    # sum = 0.0
    # array.each{ |v| sum += Math.log(v.to_f) }
    # sum /= array.size
    # Math.exp sum
  end

end

#ht_pos ⇒ Hash

Returns a hash of heterozygous variant positions as keys and allele frequency as values.

Returns:

  • (Hash) —

    a hash of heterozygous variant positions as keys and allele frequency as values



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# File 'lib/cheripic/contig.rb', line 23

class Contig

  attr_accessor :hm_pos, :ht_pos, :hemi_pos, :mean_depth, :sd_depth
  attr_reader :id, :length

  # creates a Contig object using fasta entry
  # @param fasta [Bio::FastaFormat] an individual fasta entry from input assembly file
  def initialize (fasta)
    @id = fasta.entry_id
    @length = fasta.length
    @hm_pos = {}
    @ht_pos = {}
    @hemi_pos = {}
    @mean_depth = nil
    @sd_depth = nil
  end

  # Number of homozygous variants identified in the contig
  # @return [Integer]
  def hm_num
    self.hm_pos.length
  end

  # Number of heterozygous variants identified in the contig
  # @return [Integer]
  def ht_num
    self.ht_pos.length
  end

  # Homozygosity enrichment score calculated using
  # hm_num and ht_num of the contig object
  # @return [Float]
  def hme_score
    hmes_adjust = Options.hmes_adjust
    if self.hm_num == 0 and self.ht_num == 0
      0.0
    else
      (self.hm_num + hmes_adjust) / (self.ht_num + hmes_adjust)
    end
  end

  # Number of hemi-variants identified in the contig
  # @return [Integer]
  def hemi_num
    self.hemi_pos.length
  end

  # Mean of bulk frequency ratios (bfr) calculated using
  # bfr values all hemi_pos of the contig
  # @return [Float]
  def bfr_score
    if self.hemi_pos.values.empty?
      0.0
    else
      geom_mean(self.hemi_pos.values)
    end
  end

  # Calculates mean of an array of numbers
  # @param array [Array] an array of bfr values from hemi_snp
  # @return [Float] mean value as float
  def geom_mean(array)
    return array[0].to_f if array.length == 1
    array.reduce(:+) / array.size.to_f
    # sum = 0.0
    # array.each{ |v| sum += Math.log(v.to_f) }
    # sum /= array.size
    # Math.exp sum
  end

end

#id ⇒ String (readonly)

Returns id of the contig in assembly taken from fasta file.

Returns:

  • (String) —

    id of the contig in assembly taken from fasta file



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# File 'lib/cheripic/contig.rb', line 23

class Contig

  attr_accessor :hm_pos, :ht_pos, :hemi_pos, :mean_depth, :sd_depth
  attr_reader :id, :length

  # creates a Contig object using fasta entry
  # @param fasta [Bio::FastaFormat] an individual fasta entry from input assembly file
  def initialize (fasta)
    @id = fasta.entry_id
    @length = fasta.length
    @hm_pos = {}
    @ht_pos = {}
    @hemi_pos = {}
    @mean_depth = nil
    @sd_depth = nil
  end

  # Number of homozygous variants identified in the contig
  # @return [Integer]
  def hm_num
    self.hm_pos.length
  end

  # Number of heterozygous variants identified in the contig
  # @return [Integer]
  def ht_num
    self.ht_pos.length
  end

  # Homozygosity enrichment score calculated using
  # hm_num and ht_num of the contig object
  # @return [Float]
  def hme_score
    hmes_adjust = Options.hmes_adjust
    if self.hm_num == 0 and self.ht_num == 0
      0.0
    else
      (self.hm_num + hmes_adjust) / (self.ht_num + hmes_adjust)
    end
  end

  # Number of hemi-variants identified in the contig
  # @return [Integer]
  def hemi_num
    self.hemi_pos.length
  end

  # Mean of bulk frequency ratios (bfr) calculated using
  # bfr values all hemi_pos of the contig
  # @return [Float]
  def bfr_score
    if self.hemi_pos.values.empty?
      0.0
    else
      geom_mean(self.hemi_pos.values)
    end
  end

  # Calculates mean of an array of numbers
  # @param array [Array] an array of bfr values from hemi_snp
  # @return [Float] mean value as float
  def geom_mean(array)
    return array[0].to_f if array.length == 1
    array.reduce(:+) / array.size.to_f
    # sum = 0.0
    # array.each{ |v| sum += Math.log(v.to_f) }
    # sum /= array.size
    # Math.exp sum
  end

end

#length ⇒ Integer (readonly)

Returns length of contig in bases.

Returns:

  • (Integer) —

    length of contig in bases



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# File 'lib/cheripic/contig.rb', line 23

class Contig

  attr_accessor :hm_pos, :ht_pos, :hemi_pos, :mean_depth, :sd_depth
  attr_reader :id, :length

  # creates a Contig object using fasta entry
  # @param fasta [Bio::FastaFormat] an individual fasta entry from input assembly file
  def initialize (fasta)
    @id = fasta.entry_id
    @length = fasta.length
    @hm_pos = {}
    @ht_pos = {}
    @hemi_pos = {}
    @mean_depth = nil
    @sd_depth = nil
  end

  # Number of homozygous variants identified in the contig
  # @return [Integer]
  def hm_num
    self.hm_pos.length
  end

  # Number of heterozygous variants identified in the contig
  # @return [Integer]
  def ht_num
    self.ht_pos.length
  end

  # Homozygosity enrichment score calculated using
  # hm_num and ht_num of the contig object
  # @return [Float]
  def hme_score
    hmes_adjust = Options.hmes_adjust
    if self.hm_num == 0 and self.ht_num == 0
      0.0
    else
      (self.hm_num + hmes_adjust) / (self.ht_num + hmes_adjust)
    end
  end

  # Number of hemi-variants identified in the contig
  # @return [Integer]
  def hemi_num
    self.hemi_pos.length
  end

  # Mean of bulk frequency ratios (bfr) calculated using
  # bfr values all hemi_pos of the contig
  # @return [Float]
  def bfr_score
    if self.hemi_pos.values.empty?
      0.0
    else
      geom_mean(self.hemi_pos.values)
    end
  end

  # Calculates mean of an array of numbers
  # @param array [Array] an array of bfr values from hemi_snp
  # @return [Float] mean value as float
  def geom_mean(array)
    return array[0].to_f if array.length == 1
    array.reduce(:+) / array.size.to_f
    # sum = 0.0
    # array.each{ |v| sum += Math.log(v.to_f) }
    # sum /= array.size
    # Math.exp sum
  end

end

#mean_depth ⇒ Object

Returns the value of attribute mean_depth.



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# File 'lib/cheripic/contig.rb', line 25

def mean_depth
  @mean_depth
end

#sd_depth ⇒ Object

Returns the value of attribute sd_depth.



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# File 'lib/cheripic/contig.rb', line 25

def sd_depth
  @sd_depth
end

Instance Method Details

#bfr_score ⇒ Float

Mean of bulk frequency ratios (bfr) calculated using bfr values all hemi_pos of the contig

Returns:

  • (Float) 


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# File 'lib/cheripic/contig.rb', line 73

def bfr_score
  if self.hemi_pos.values.empty?
    0.0
  else
    geom_mean(self.hemi_pos.values)
  end
end

#geom_mean(array) ⇒ Float

Calculates mean of an array of numbers

Parameters:

  • array (Array) —

    an array of bfr values from hemi_snp

Returns:

  • (Float) —

    mean value as float



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# File 'lib/cheripic/contig.rb', line 84

def geom_mean(array)
  return array[0].to_f if array.length == 1
  array.reduce(:+) / array.size.to_f
  # sum = 0.0
  # array.each{ |v| sum += Math.log(v.to_f) }
  # sum /= array.size
  # Math.exp sum
end

#hemi_num ⇒ Integer

Number of hemi-variants identified in the contig

Returns:

  • (Integer) 


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# File 'lib/cheripic/contig.rb', line 66

def hemi_num
  self.hemi_pos.length
end

#hm_num ⇒ Integer

Number of homozygous variants identified in the contig

Returns:

  • (Integer) 


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# File 'lib/cheripic/contig.rb', line 42

def hm_num
  self.hm_pos.length
end

#hme_score ⇒ Float

Homozygosity enrichment score calculated using hm_num and ht_num of the contig object

Returns:

  • (Float) 


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# File 'lib/cheripic/contig.rb', line 55

def hme_score
  hmes_adjust = Options.hmes_adjust
  if self.hm_num == 0 and self.ht_num == 0
    0.0
  else
    (self.hm_num + hmes_adjust) / (self.ht_num + hmes_adjust)
  end
end

#ht_num ⇒ Integer

Number of heterozygous variants identified in the contig

Returns:

  • (Integer) 


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# File 'lib/cheripic/contig.rb', line 48

def ht_num
  self.ht_pos.length
end