Class: MutationSet::Sample

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

Direct Known Subclasses

Indelocator, Maf, MuTect, VCF

Class Attribute Summary collapse

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(mutation_config = nil, suppress_headers = nil) ⇒ Sample

Returns a new instance of Sample.



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# File 'lib/mutation_set.rb', line 289

def initialize(mutation_config=nil,suppress_headers=nil)
  @lines = []

  @mutation_config = YAML.load_file(mutation_config) if mutation_config

  @headers = required.map(&:to_sym) unless suppress_headers

  @preamble_lines = []

  @index = {}
end

Class Attribute Details

.comment ⇒ Object (readonly)

Returns the value of attribute comment.



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# File 'lib/mutation_set.rb', line 187

def comment
  @comment
end

.required ⇒ Object (readonly)

Returns the value of attribute required.



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# File 'lib/mutation_set.rb', line 187

def required
  @required
end

Instance Attribute Details

#headers ⇒ Object

Returns the value of attribute headers.



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# File 'lib/mutation_set.rb', line 185

def headers
  @headers
end

#lines ⇒ Object (readonly)

Returns the value of attribute lines.



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# File 'lib/mutation_set.rb', line 184

def lines
  @lines
end

#mutation_config ⇒ Object (readonly)

Returns the value of attribute mutation_config.



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# File 'lib/mutation_set.rb', line 184

def mutation_config
  @mutation_config
end

#preamble_lines ⇒ Object (readonly)

Returns the value of attribute preamble_lines.



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# File 'lib/mutation_set.rb', line 184

def preamble_lines
  @preamble_lines
end

#samples ⇒ Object (readonly)

Returns the value of attribute samples.



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# File 'lib/mutation_set.rb', line 184

def samples
  @samples
end

Class Method Details

.comments(c) ⇒ Object 



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# File 'lib/mutation_set.rb', line 192

def comments c
  @comment = c
end

.read(filename, mutation_config = nil) ⇒ Object 



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# File 'lib/mutation_set.rb', line 196

def read(filename,mutation_config=nil)
  set = new mutation_config, true

  set.load_file filename

  return set
end

.requires(*terms) ⇒ Object 



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# File 'lib/mutation_set.rb', line 188

def requires *terms
  @required = terms
end

Instance Method Details

#[](key) ⇒ Object 



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# File 'lib/mutation_set.rb', line 333

def [](key)
  @lines[key]
end

#add_line(fields) ⇒ Object 



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# File 'lib/mutation_set.rb', line 262

def add_line fields
  @lines.push self.class.const_get(:Line).new(clean_fields(fields), self)

  index_line @lines.last
end

#blacklist(file) ⇒ Object 



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# File 'lib/mutation_set.rb', line 313

def blacklist file
  case file
  when /.gtf$/
    require 'gtf'
    @blacklist ||= GTF.new(file).to_interval_list
  when /.vcf$/
    require 'vcf'
    @blacklist ||= VCF.read(file).to_interval_list
  end
  @blacklist
end

#clean_fields(fields) ⇒ Object 



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# File 'lib/mutation_set.rb', line 268

def clean_fields fields
  fields.is_a?(Array) ? fields.map{|f| f == "NA" ? "" : f } : fields
end

#clean_header(s) ⇒ Object 



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# File 'lib/mutation_set.rb', line 254

def clean_header s
  s.to_s.gsub(/\s+/,"_").gsub(/[^\w]+/,"").downcase.to_sym
end

#clean_headers ⇒ Object 



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# File 'lib/mutation_set.rb', line 258

def clean_headers
  @headers.map {|h| clean_header h}
end

#each ⇒ Object 



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# File 'lib/mutation_set.rb', line 341

def each
  @lines.each do |l|
    yield l
  end
end

#enforce_headers(array) ⇒ Object 



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# File 'lib/mutation_set.rb', line 284

def enforce_headers array
  raise "File lacks required headers: #{(required.map(&:downcase)-array.map(&:downcase)).join(", ")}" if !(required.map(&:downcase) - array.map(&:downcase)).empty?
  @headers = array
end

#find_mutation(line) ⇒ Object 



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# File 'lib/mutation_set.rb', line 276

def find_mutation line
  @index[ line.key ]
end

#format_line(l) ⇒ Object 



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# File 'lib/mutation_set.rb', line 250

def format_line l
  l.to_s
end

#index_line(line) ⇒ Object 



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# File 'lib/mutation_set.rb', line 272

def index_line line
  @index[ line.key ] = line
end

#inspect ⇒ Object 



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# File 'lib/mutation_set.rb', line 329

def inspect
  to_s
end

#load_file(filename) ⇒ Object 



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# File 'lib/mutation_set.rb', line 205

def load_file filename
  File.foreach(filename) do |l|
    fields = l.chomp.split(/\t/,-1)
    if !headers
      if fields.first.downcase == required.first.downcase
        enforce_headers fields
      else
        preamble_lines.push l
      end
      next
    end
    add_line fields
  end

  post_read_hook
end

#output(f) ⇒ Object 



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# File 'lib/mutation_set.rb', line 240

def output f
  f.puts preamble
  f.puts headers.join("\t")
  @lines.each do |l|
    l = yield l if block_given?
    next if !l || l.invalid?
    f.puts format_line(l)
  end
end

#preamble ⇒ Object 



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# File 'lib/mutation_set.rb', line 222

def preamble
  preamble_lines.join("")
end

#print(f = nil) ⇒ Object 



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# File 'lib/mutation_set.rb', line 232

def print f=nil
  if f
    write f
  else
    output STDOUT
  end
end

#required ⇒ Object 



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# File 'lib/mutation_set.rb', line 280

def required
  self.class.required
end

#sort_by!(&block) ⇒ Object 



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# File 'lib/mutation_set.rb', line 337

def sort_by! &block
  @lines.sort_by! &block
end

#to_interval_list ⇒ Object 



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# File 'lib/mutation_set.rb', line 325

def to_interval_list
  IntervalList.new self.map{|g| [ g.chrom, g.start, g.stop, g ] }
end

#whitelist(file) ⇒ Object 



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# File 'lib/mutation_set.rb', line 301

def whitelist file
  case file
  when /.gtf$/
    require 'gtf'
    @whitelist ||= GTF.new(file).to_interval_list
  when /.vcf$/
    require 'vcf'
    @whitelist ||= VCF.read(file).to_interval_list
  end
  @whitelist
end

#write(file) ⇒ Object 



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# File 'lib/mutation_set.rb', line 226

def write file
  File.open(file,"w") do |f|
    output f
  end
end