Class: Bioinform::MatrixParser

Inherits:
Object
  • Object
show all
Defined in:
lib/bioinform/parsers/matrix_parser.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(options = {}) ⇒ MatrixParser

Returns a new instance of MatrixParser.

Raises:



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# File 'lib/bioinform/parsers/matrix_parser.rb', line 7

def initialize(options = {})
  @has_name = options.fetch(:has_name, :auto)
  @name_pattern = options.fetch(:name_pattern, /^>?\s*(?<name>[^-+\d.\t\r\n][^\t\r\n]*).*$/)
  @has_header_row = options.fetch(:has_header_row, false)
  @has_header_column = options.fetch(:has_header_column, false)
  @nucleotides_in = options.fetch(:nucleotides_in, :auto)
  @fix_nucleotides_number = options.fetch(:fix_nucleotides_number, 4)

  raise Error, ':nucleotides_in option should be either :rows or :columns' unless  [:rows, :columns, :auto].include?(@nucleotides_in)
end

Instance Attribute Details

#fix_nucleotides_number ⇒ Object (readonly)

fix_nucleotides_number – raises if matrix has not enough nucleotide columns



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# File 'lib/bioinform/parsers/matrix_parser.rb', line 6

def fix_nucleotides_number
  @fix_nucleotides_number
end

#has_header_column ⇒ Object (readonly)

fix_nucleotides_number – raises if matrix has not enough nucleotide columns



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# File 'lib/bioinform/parsers/matrix_parser.rb', line 6

def has_header_column
  @has_header_column
end

#has_header_row ⇒ Object (readonly)

fix_nucleotides_number – raises if matrix has not enough nucleotide columns



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# File 'lib/bioinform/parsers/matrix_parser.rb', line 6

def has_header_row
  @has_header_row
end

#has_name ⇒ Object (readonly)

fix_nucleotides_number – raises if matrix has not enough nucleotide columns



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# File 'lib/bioinform/parsers/matrix_parser.rb', line 6

def has_name
  @has_name
end

#name_pattern ⇒ Object (readonly)

fix_nucleotides_number – raises if matrix has not enough nucleotide columns



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# File 'lib/bioinform/parsers/matrix_parser.rb', line 6

def name_pattern
  @name_pattern
end

#nucleotides_in ⇒ Object (readonly)

fix_nucleotides_number – raises if matrix has not enough nucleotide columns



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# File 'lib/bioinform/parsers/matrix_parser.rb', line 6

def nucleotides_in
  @nucleotides_in
end

Instance Method Details

#parse(input) ⇒ Object 



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# File 'lib/bioinform/parsers/matrix_parser.rb', line 63

def parse(input)
  parse!(input) rescue nil
end

#parse!(input) ⇒ Object 



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# File 'lib/bioinform/parsers/matrix_parser.rb', line 23

def parse!(input)
  lines = input.strip.lines.to_a
  if @has_name == :auto
    match = lines.first.match(@name_pattern)
    if match
      lines.shift
      name = match[:name]
    end
  elsif @has_name == false
    name = nil
  else
    match = lines.shift.match(@name_pattern)
    raise Error, "Name pattern doesn't match"  unless match
    name = match[:name]
  end
  lines.shift  if @has_header_row
  matrix = lines.map(&:rstrip).reject(&:empty?).map{|line| line.split }
  matrix = matrix.map{|row| row.drop(1) }  if @has_header_column
  matrix = matrix.map{|row| row.map{|el| Float(el) } }

  case @nucleotides_in
  when :columns
    matrix = matrix
  when :rows
    matrix = matrix.transpose
  when :auto
    if @fix_nucleotides_number && need_transpose?(matrix)
      matrix = matrix.transpose
    end
  end

  if @fix_nucleotides_number
    raise Error, 'Not enough nucleotides in a matrix'  unless matrix.all?{|pos| pos.size >= @fix_nucleotides_number}
    matrix = matrix.map{|pos| pos.first(@fix_nucleotides_number) }
  end
  {matrix: matrix, name: name}
rescue => e
  raise Error, e.message
end

#valid?(input) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/bioinform/parsers/matrix_parser.rb', line 67

def valid?(input)
  result = parse!(input)
rescue
  false
end