Class: MutationSet::Line

Inherits:
Object
  • Object
show all
Includes:
IntervalList::Interval
Defined in:
lib/mutation_set.rb

Direct Known Subclasses

Indelocator::Line, Maf::Line, MuTect::Line, VCF::Line

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from IntervalList::Interval

#above?, #below?, #center, #clone, #contains?, #dist, #intersect, #intersection_size, #nearest, #overlap, #overlaps?, #size, #strict_diff, #strict_overlap, #strict_union

Constructor Details

#initialize(fields, sample) ⇒ Line

Returns a new instance of Line.



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# File 'lib/mutation_set.rb', line 33

def initialize(fields, sample)
  if fields.is_a? Hash
    @mutation = fields
  else
    @mutation = Hash[sample.clean_headers.zip(fields)]
  end
  @sample = sample
end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method

#method_missing(meth, *args, &block) ⇒ Object 



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# File 'lib/mutation_set.rb', line 157

def method_missing(meth,*args,&block)
  if meth.to_s =~ /(.*)=/ 
    @mutation[$1.to_sym] = args.first
  else
    @mutation.has_key?(meth.to_sym) ? @mutation[meth.to_sym] : super
  end
end

Instance Attribute Details

#invalid ⇒ Object

Returns the value of attribute invalid.



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# File 'lib/mutation_set.rb', line 9

def invalid
  @invalid
end

#sample ⇒ Object (readonly)

Returns the value of attribute sample.



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# File 'lib/mutation_set.rb', line 8

def sample
  @sample
end

Class Method Details

.alias_key(sym1, sym2) ⇒ Object 



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# File 'lib/mutation_set.rb', line 11

def self.alias_key sym1, sym2
  define_method sym1 do
    send sym2
  end
  define_method "#{sym1}=" do |v|
    send "#{sym2}=", v
  end
end

Instance Method Details

#copy ⇒ Object 



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# File 'lib/mutation_set.rb', line 20

def copy
  self.class.new @mutation.clone, sample
end

#criteria_failed?(obj, name) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/mutation_set.rb', line 63

def criteria_failed? obj, name
  return nil if !sample.mutation_config
  name = [ name ] if !name.is_a? Array
  crit = name.reduce(sample.mutation_config) do |h,n|
    h.is_a?(Hash) ? h[n] : nil
  end
  return nil if !crit
  crit.each do |attrib,value|
    return true if !criterion_ok? obj, attrib, value
  end
  nil
end

#criterion_ok?(obj, attrib, value) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/mutation_set.rb', line 76

def criterion_ok? obj, attrib, value
  case attrib
  when /^min_(.*)/
    v = obj.send($1.to_sym).to_f
    return v >= value.to_f
  when /^max_(.*)/
    return obj.send($1.to_sym).to_f <= value.to_f
  when /^exclude_(.*)/
    v = obj.send($1.to_sym)
    if value.is_a? Array
      return value.none? { |r| v.match(/#{r}/) }
    else
      return v !~ /#{value}/
    end
  when /^has_(.*)/
    v = obj.send($1.to_sym)
    if value.is_a? Array
      return value.include? v
    elsif value == true
      return v && (v.is_a?(String) ? v.size > 0 : v)
    elsif value == false || value == "nil"
      return !v
    else
      return value == v
    end
  when /^include_(.*)/
    v = obj.send($1.to_sym)
    if value.is_a? Array
      return value.any? { |r| v.match(/#{r}/) }
    else
      return v =~ /#{value}/
    end
  when /^either.*/
    v = nil
    value.each do |attrib,val|
      v = true if criterion_ok? obj, attrib, val
    end
    return v
  when /^whitelisted/
    whitelist = sample.whitelist value
    return whitelist.intersect(self)
  when /^blacklisted/
    blacklist = sample.blacklist value
    return !blacklist.intersect(self)
  else
    # send it
    case value
    when "nil", false, nil
    return !obj.send(attrib.to_sym)
    when true
    return obj.send(attrib.to_sym)
    end
  end
  true
end

#discard_onco ⇒ Object 



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# File 'lib/mutation_set.rb', line 137

def discard_onco
  @onco = nil
end

#in_cosmic ⇒ Object 



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# File 'lib/mutation_set.rb', line 149

def in_cosmic
  onco.Cosmic_overlapping_mutations ? "YES" : "NO"
end

#inspect ⇒ Object 



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# File 'lib/mutation_set.rb', line 145

def inspect
  "#<#{self.class.name}:#{object_id} @mutation=#{@mutation}>"
end

#invalid? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/mutation_set.rb', line 24

def invalid?
  invalid
end

#invalidate! ⇒ Object 



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# File 'lib/mutation_set.rb', line 28

def invalidate!
  @invalid = true
end

#key ⇒ Object 



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# File 'lib/mutation_set.rb', line 42

def key
  "#{chrom}:#{start}:#{stop}"
end

#long_chrom ⇒ Object 



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# File 'lib/mutation_set.rb', line 46

def long_chrom
  @long_chrom ||= "chr#{short_chrom}"
end

#onco ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/mutation_set.rb', line 132

def onco
  raise ArgumentError, @onco_error unless valid_onco_input?
  @onco ||= Oncotator.new :key => self.to_ot
end

#respond_to?(method) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/mutation_set.rb', line 165

def respond_to? method
  !@mutation[method.to_sym].nil? || super
end

#short_chrom ⇒ Object 



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# File 'lib/mutation_set.rb', line 50

def short_chrom
  @short_chrom ||= chrom.sub(/^chr/,'')
end

#skip_oncotator?(criteria = nil) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/mutation_set.rb', line 141

def skip_oncotator? criteria=nil
  return true if !onco || onco.empty? || criteria_failed?(onco, criteria || :oncotator)
end

#to_hash ⇒ Object 



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# File 'lib/mutation_set.rb', line 58

def to_hash
  @mutation
  #Hash[@mutation.map do |k,v| [ k, v ? v.clone : v ]; end]
end

#to_ot ⇒ Object 



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# File 'lib/mutation_set.rb', line 153

def to_ot
  [ short_chrom, start, stop, ref_allele, alt_allele ].join("_")
end

#to_s ⇒ Object 



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# File 'lib/mutation_set.rb', line 54

def to_s
  sample.clean_headers.map{ |h| @mutation[h] }.join("\t")
end