Class: TransfacFormatter

Inherits:
Object show all
Defined in:
lib/bioinform/formatters/transfac_formatter.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(motif, options = {}) ⇒ TransfacFormatter 



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# File 'lib/bioinform/formatters/transfac_formatter.rb', line 4

def initialize(motif, options = {})
  @motif = motif
  
  default_options = {with_name: true, letters_as_rows: false}
  @options = default_options.merge(options)
end

Instance Attribute Details

#motif ⇒ Object

Returns the value of attribute motif.



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# File 'lib/bioinform/formatters/transfac_formatter.rb', line 2

def motif
  @motif
end

#options ⇒ Object

Returns the value of attribute options.



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# File 'lib/bioinform/formatters/transfac_formatter.rb', line 2

def options
  @options
end

Instance Method Details



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# File 'lib/bioinform/formatters/transfac_formatter.rb', line 31

def footer
  #"XX\n//\n"

  "\nXX\n//"
end

#header ⇒ Object 



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# File 'lib/bioinform/formatters/transfac_formatter.rb', line 15

def header
  if options[:with_name] && name
    "ID #{name}\nBF StubSpeciesName\nP0\tA\tC\tG\tT\n"
  else
    raise 'Transfac should have the name field'
  end
end

#matrix_string ⇒ Object 



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# File 'lib/bioinform/formatters/transfac_formatter.rb', line 23

def matrix_string
  motif.each_position.map.with_index{|pos,ind| 
    line_number = ind.to_s
    line_number = (line_number.size == 1) ? "0#{line_number}" : line_number
    line_number + ' ' + pos.join("\t")
  }.join("\n")
end

#name ⇒ Object 



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# File 'lib/bioinform/formatters/transfac_formatter.rb', line 11

def name
  motif.name
end

#to_s ⇒ Object 



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# File 'lib/bioinform/formatters/transfac_formatter.rb', line 36

def to_s
  header + matrix_string + footer
end