class Bio::DB::Vcf

Attributes

alt[RW]

chrom[RW]

filter[RW]

format[RW]

id[RW]

info[RW]

pos[RW]

qual[RW]

ref[RW]

samples[RW]

Public Class Methods

new(line=nil, sample_names=nil) click to toggle source

create the vcf object, use the ordered list of sample names to label samples if provided ['A', 'B', 'C'], otherwise uses, 1,2,3 etc

vcf = Bio::DB::Vcf("19       111   . A       C     9.6 .       .     GT:HQ       0|0:10,10     0|0:10,10   0/1:3,3")

# File lib/bio/db/vcf.rb, line 15
def initialize(line=nil, sample_names=nil)
  @info = {}
  @samples = {}
  parse_line(line, sample_names) if line != nil
end

Public Instance Methods

int_or_raw(x) click to toggle source

tests if the current variable is an Integer

x - any variable

# File lib/bio/db/vcf.rb, line 23
def int_or_raw(x)
  Integer.new(x) rescue x
end

parse_line(line, sample_names=nil) click to toggle source

gets the info in the Vcf lines and parses it, setting the attributes

# File lib/bio/db/vcf.rb, line 28
def parse_line(line, sample_names=nil)
  return false if line[0,1] == '#'
    
  f = line.chomp.split("\t", -1)
  raise "VCF lines must have at least 8 fields" if f.size < 8
  @chrom = f[0]
  @pos = f[1].to_i
  @id =  '.' == f[2] ? nil : f[2]
  @ref = f[3]
  @alt = f[4]
  @qual = f[5].to_f
  @filter = '.' == f[6] ? nil : f[6]
    
  @info = '.' == f[7] ? nil : {}
  if @info
    info_vec = f[7].split(";")
    info_vec.each do |x|
      keyval = x.split("=", -1)
      if keyval.size == 2 # If it's key=value
        @info[keyval[0]] = keyval[1]
      else # Otherwise, it's just a flag
        @info[x] = nil
      end
    end
  end
    
  @samples = {}
  return true if f.size == 8  # Has just upto info
  raise "Can't have format with no samples" if f.size == 9
  
  @format = f[8]
    
  sample_keys = @format.split(":")
    
  num_samples = f.size - 9 # How many fields are past the format
    
  if sample_names == nil # Make the sample names just ["1", "2", ... , "num_samples}"
    sample_names = (1..num_samples).to_a.map{|i| i.to_s} 
  elsif sample_names.size != num_samples
    raise "Unexpected number of samples (#{num_samples}) based on the provided sample names (#{sample_names.inspect})"
  end
    
  sample_names.each_with_index do |sample_name, sample_index|
    i = sample_index + 9 # index into columns (f)
    sample_values = f[i].split(":")
    raise "Expected number of sample values to be <= number of sample keys in FORMAT column Format=#{@format} but sample=#{f[i]}" if sample_values.size > sample_keys.size
    @samples[sample_name] = {}
    sample_keys.each_with_index {|key, value_index| @samples[sample_name][key] = sample_values[value_index] || ""}
  end
  
  return true;
end