Module: Bio::RestrictionEnzyme::StringFormatting

Extended by:
CutSymbol
Includes:
CutSymbol
Included in:
DoubleStranded, DoubleStranded, DoubleStranded::AlignedStrands, Range::SequenceRange::CalculatedCuts, SingleStrand
Defined in:
lib/bio/util/restriction_enzyme/string_formatting.rb

Instance Method Summary collapse

Methods included from CutSymbol

cut_symbol, escaped_cut_symbol, re_cut_symbol, re_cut_symbol_adjacent, set_cut_symbol

Instance Method Details

#add_spacing(seq, cs = cut_symbol) ⇒ Object

Return the sequence with spacing for alignment. Does not add whitespace around cut symbols.

Example:

pattern = 'n^ng^arraxt^n'
add_spacing( pattern )      # => "n^n g^a r r a x t^n"

Arguments

  • seq: sequence with cut symbols

  • cs: (optional) Cut symbol along the string. The reason this is definable outside of CutSymbol is that this is a utility function used to form vertical and horizontal cuts such as:

    a|t g c
 +---+
t a c|g
Returns

String sequence with single character distance between bases



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# File 'lib/bio/util/restriction_enzyme/string_formatting.rb', line 30

def add_spacing( seq, cs = cut_symbol )
  str = ''
  flag = false
  seq.each_byte do |c|
    c = c.chr
    if c == cs
      str += c
      flag = false
    elsif flag
      str += ' ' + c
    else
      str += c
      flag = true
    end
  end
  str
end

#left_padding(s) ⇒ Object

Return the ‘n’ padding on the left side of the strand

Arguments

  • s: sequence with extraneous ‘n’ padding on the left side of the strand

Returns

String the ‘n’ padding from the left side



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# File 'lib/bio/util/restriction_enzyme/string_formatting.rb', line 84

def left_padding( s )
  s =~ %r{^n+}
  ret = $&
  ret ? ret : ''  # Don't pass nil values
end

#right_padding(s) ⇒ Object

Return the ‘n’ padding on the right side of the strand

Arguments

  • s: sequence with extraneous ‘n’ padding on the right side of the strand

Returns

String the ‘n’ padding from the right side



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# File 'lib/bio/util/restriction_enzyme/string_formatting.rb', line 96

def right_padding( s )
  s =~ %r{n+$}
  ret = $&
  ret ? ret : ''  # Don't pass nil values
end

#strip_cuts_and_padding(s) ⇒ Object

Remove extraneous nucleic acid wildcards (‘n’ padding) from the left and right sides and remove cut symbols

Arguments

  • s: sequence with extraneous ‘n’ padding and cut symbols

Returns

String sequence without ‘n’ padding on the sides or cut symbols



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# File 'lib/bio/util/restriction_enzyme/string_formatting.rb', line 74

def strip_cuts_and_padding( s )
  strip_padding( s.tr(cut_symbol, '') )
end

#strip_padding(s) ⇒ Object

Remove extraneous nucleic acid wildcards (‘n’ padding) from the left and right sides

Arguments

  • s: sequence with extraneous ‘n’ padding

Returns

String sequence without ‘n’ padding on the sides



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# File 'lib/bio/util/restriction_enzyme/string_formatting.rb', line 55

def strip_padding( s )
  if s[0].chr == 'n'
    s =~ %r{(n+)(.+)}
    s = $2
  end
  if s[-1].chr == 'n'
    s =~ %r{(.+?)(n+)$}
    s = $1
  end
  s
end