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

[Source]

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

left_padding( s )

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 92
92:   def left_padding( s )
93:     s =~ %r{^n+}
94:     ret = $&
95:     ret ? ret : ''  # Don't pass nil values
96:   end

right_padding( s )

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 104
104:   def right_padding( s )
105:     s =~ %r{n+$}
106:     ret = $&
107:     ret ? ret : ''  # Don't pass nil values
108:   end

strip_cuts_and_padding( s )

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 82
82:   def strip_cuts_and_padding( s )
83:     strip_padding( s.tr(cut_symbol, '') )
84:   end

strip_padding( s )

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 63
63:   def strip_padding( s )
64:     if s[0].chr == 'n'
65:       s =~ %r{(n+)(.+)}
66:       s = $2
67:     end
68:     if s[-1].chr == 'n'
69:       s =~ %r{(.+?)(n+)$}
70:       s = $1
71:     end
72:     s
73:   end

Methods

Included Modules

Public Instance methods