Module Bio::RestrictionEnzyme::StringFormatting
In: lib/bio/util/restriction_enzyme/string_formatting.rb

Methods

Included Modules

CutSymbol

Public Instance methods

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

[Source]

    # File lib/bio/util/restriction_enzyme/string_formatting.rb, line 37
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

[Source]

    # File lib/bio/util/restriction_enzyme/string_formatting.rb, line 91
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

[Source]

     # File lib/bio/util/restriction_enzyme/string_formatting.rb, line 103
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

[Source]

    # File lib/bio/util/restriction_enzyme/string_formatting.rb, line 81
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

[Source]

    # File lib/bio/util/restriction_enzyme/string_formatting.rb, line 62
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

[Validate]