module Bio::RestrictionEnzyme::StringFormatting

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

   # File lib/bio/util/restriction_enzyme/string_formatting.rb
37 def add_spacing( seq, cs = cut_symbol )
38   str = ''
39   flag = false
40   seq.each_byte do |c|
41     c = c.chr
42     if c == cs
43       str += c
44       flag = false
45     elsif flag
46       str += ' ' + c
47     else
48       str += c
49       flag = true
50     end
51   end
52   str
53 end

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

   # File lib/bio/util/restriction_enzyme/string_formatting.rb
91 def left_padding( s )
92   s =~ %r{^n+}
93   ret = $&
94   ret ? ret : ''  # Don't pass nil values
95 end

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

    # File lib/bio/util/restriction_enzyme/string_formatting.rb
103 def right_padding( s )
104   s =~ %r{n+$}
105   ret = $&
106   ret ? ret : ''  # Don't pass nil values
107 end

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

   # File lib/bio/util/restriction_enzyme/string_formatting.rb
81 def strip_cuts_and_padding( s )
82   strip_padding( s.tr(cut_symbol, '') )
83 end

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

   # File lib/bio/util/restriction_enzyme/string_formatting.rb
62 def strip_padding( s )
63   if s[0].chr == 'n'
64     s =~ %r{(n+)(.+)}
65     s = $2
66   end
67   if s[-1].chr == 'n'
68     s =~ %r{(.+?)(n+)$}
69     s = $1
70   end
71   s
72 end