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#
# bio/util/restriction_enzyme/string_formatting.rb - Useful functions for string manipulation
#
# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
# License:: The Ruby License
#
module Bio
require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
class RestrictionEnzyme
module StringFormatting
include CutSymbol
extend CutSymbol
# 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
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
# 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
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
# 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
def strip_cuts_and_padding( s )
strip_padding( s.tr(cut_symbol, '') )
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
def left_padding( s )
s =~ %r{^n+}
ret = $&
ret ? ret : '' # Don't pass nil values
end
# Return the 'n' padding on the right side of the strand
#
# ---
# *Arguments*
# * +s+: sequence with extraneous 'n' padding on the right side of the strand
# *Returns*:: +String+ the 'n' padding from the right side
def right_padding( s )
s =~ %r{n+$}
ret = $&
ret ? ret : '' # Don't pass nil values
end
end # StringFormatting
end # RestrictionEnzyme
end # Bio
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