Class: Bio::DB::Vcf

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/util/bio-gngm.rb

Overview

Extends the methods of the Bio::DB::Vcf class in bio-samtools. A Vcf object represents the VCF format described at www.1000genomes.org/node/101 . The Bio::DB::Vcf object returns all information in the VCF line, but the implementation here acts as if there is only possibly one variant at each position and ignores positions at which there may be multiple variants. Vcf format is only used when the Bio::Util::Gngm object requests information about indels using SAMtools mpileup method.

Instance Method Summary collapse

Instance Method Details

#alternatives ⇒ Object

List of alternate alleles at this locus, obtained by splitting the vcf.alt attribute string on commas

Example vcf.alt = “ACT,TCA” vcf.alternatives = [“ACT”, “TCA”] vcf.alt = “T” vcf.alternatives = [“T”]



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# File 'lib/bio/util/bio-gngm.rb', line 123

def alternatives
  self.alt.split(",") rescue []
end

#gq ⇒ Object

Returns the genotype quality score from the sample data (as defined by the Vcf GQ attribute) for the first sample in the Vcf only.



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# File 'lib/bio/util/bio-gngm.rb', line 146

def gq 
  self.samples["1"]["GQ"].to_f rescue 0.0
end

#is_indel?(options) ⇒ Boolean

Returns true if ref col is different in length from any of the entries in alt column

Returns:

  • (Boolean) 


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# File 'lib/bio/util/bio-gngm.rb', line 186

def is_indel?(options)
  return true if self.variant? and self.alternatives.any? {|x| x.length != self.ref.length} and self.pass_quality?(options)
  false
end

#is_mnp?(options) ⇒ Boolean

returns true if ref col has same length as all alternatives and position variant passes quality

Returns:

  • (Boolean) 


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# File 'lib/bio/util/bio-gngm.rb', line 174

def is_mnp?(options)
  return true if self.alternatives.all? {|x| x.length == self.ref.length} and self.pass_quality?(options)
  false
end

#is_snp?(options) ⇒ Boolean

returns true if ref col has length of 1 and is_mnp?

Returns:

  • (Boolean) 


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# File 'lib/bio/util/bio-gngm.rb', line 180

def is_snp?(options)
  return true if self.is_mnp?(options) and self.ref.length == 1
  false
end

#mq ⇒ Object

Returns the mean Mapping Quality from the reads over this position as defined by the Vcf MQ attribute.



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# File 'lib/bio/util/bio-gngm.rb', line 141

def mq
  self.info["MQ"].to_f rescue 0.0
end

#non_ref_allele_count ⇒ Object

Returns the depth of reads containing the non reference allele. IE the sum of the last two figures in the DP4 attribute.



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# File 'lib/bio/util/bio-gngm.rb', line 128

def non_ref_allele_count
  self.info["DP4"].split(",")[2..3].inject {|sum,n| sum.to_f + n.to_f } rescue 0.0
end

#non_ref_allele_freq ⇒ Object

Returns the non-reference allele frequency based on depth of reads used for the genotype call,

IE vcf.non_ref_allele_count / vcf.used_depth



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# File 'lib/bio/util/bio-gngm.rb', line 136

def non_ref_allele_freq
  self.non_ref_allele_count / self.used_depth
end

#pass_quality?(options) ⇒ Boolean

Returns true if the position passes criteria

Options and Defaults:

  • :min_depth => 2

  • :min_non_ref_count => 2

  • :mapping_quality => 10

Example vcf.pass_quality?(:min_depth => 5, :min_non_ref_count => 2, :mapping_quality => 25, :min_snp_quality => 20)

Returns:

  • (Boolean) 


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# File 'lib/bio/util/bio-gngm.rb', line 169

def pass_quality?(options)
  (self.used_depth >= options[:min_depth] and self.mq >= options[:mapping_quality] and self.non_ref_allele_count >= options[:min_non_ref_count] and self.qual >= options[:min_snp_quality])
end

#pl ⇒ Object

Returns the phred scaled likelihood of the first non-reference allele (as defined by the Vcf PL attribute) for the first sample in the Vcf only.



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# File 'lib/bio/util/bio-gngm.rb', line 151

def pl
  self.samples["1"]["PL"].split(",")[1].to_f rescue 0.0
end

#to_s ⇒ Object

Return a short string representing chromosome, position, reference sequence, alt sequence(s) and the info string of the Vcf object.



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# File 'lib/bio/util/bio-gngm.rb', line 107

def to_s
  "#{self.chrom} #{self.pos} #{self.ref} #{self.alt} #{self.info}"
end

#used_depth ⇒ Object

The depth of reads actually used in the genotype call by Vcftools. The sum of the DP4 attribute. Returns 0.0 if no value is calculated.



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# File 'lib/bio/util/bio-gngm.rb', line 112

def used_depth
  self.info["DP4"].split(",").inject {|sum,n| sum.to_f + n.to_f} rescue 0.0
end

#variant? ⇒ Boolean

returns true if the alt column of the Vcf is not .

Examples

vcf record = 20 14370 rs6054257 G A 29 PASS … vcf.variant? #=> true vcf record = 20 1230237 . T . 47 PASS … vcf.variant? #=> false

Returns:

  • (Boolean) 


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# File 'lib/bio/util/bio-gngm.rb', line 102

def variant?
  not self.alt == "." rescue false
end