Class: Bio::DB::Vcf

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

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(line = nil, sample_names = nil) ⇒ Vcf

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")



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# 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

Instance Attribute Details

#alt ⇒ Object

Returns the value of attribute alt.



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# File 'lib/bio/db/vcf.rb', line 11

def alt
  @alt
end

#chrom ⇒ Object

Returns the value of attribute chrom.



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# File 'lib/bio/db/vcf.rb', line 11

def chrom
  @chrom
end

#filter ⇒ Object

Returns the value of attribute filter.



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# File 'lib/bio/db/vcf.rb', line 11

def filter
  @filter
end

#format ⇒ Object

Returns the value of attribute format.



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# File 'lib/bio/db/vcf.rb', line 11

def format
  @format
end

#id ⇒ Object

Returns the value of attribute id.



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# File 'lib/bio/db/vcf.rb', line 11

def id
  @id
end

#info ⇒ Object

Returns the value of attribute info.



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# File 'lib/bio/db/vcf.rb', line 11

def info
  @info
end

#pos ⇒ Object

Returns the value of attribute pos.



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# File 'lib/bio/db/vcf.rb', line 11

def pos
  @pos
end

#qual ⇒ Object

Returns the value of attribute qual.



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# File 'lib/bio/db/vcf.rb', line 11

def qual
  @qual
end

#ref ⇒ Object

Returns the value of attribute ref.



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# File 'lib/bio/db/vcf.rb', line 11

def ref
  @ref
end

#samples ⇒ Object

Returns the value of attribute samples.



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# File 'lib/bio/db/vcf.rb', line 11

def samples
  @samples
end

Instance Method Details

#int_or_raw(x) ⇒ Object

tests if the current variable is an Integer

  • x - any variable



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# 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) ⇒ Object

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



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# File 'lib/bio/db/vcf.rb', line 51

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

#to_s ⇒ Object

returns vcf format line



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# File 'lib/bio/db/vcf.rb', line 28

def to_s
  if !@chrom.nil? 
    str = [@chrom, @pos, @id, @ref, @alt, @qual.to_i, @filter, ""].join("\t")
    #@format, @samples]
    infos=[]
    info.each do|key,val|
      infos << "#{key}=#{val}"
    end
    str << infos.join(";")
    str << "\t#{@format}\t"
    samples.each do |key, val|
      array=[]
      val.each do |keys, vals|
        array << "#{vals}"
      end
      str << array.join(":")
      str << "\t"
    end
  end
  str
end