1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
|
#
# Extensions of the String class to handle nucleotidic sequences
#
module RGFA::Sequence
# Computes the reverse complement of a nucleotidic sequence
#
# @return [String] reverse complement, without newlines and spaces
# @return [String] "*" if string is "*"
#
# @param tolerant [Boolean] <i>(defaults to: +false+)</i>
# if true, anything non-sequence is complemented to itself
# @param rnasequence [Boolean] <i>(defaults to: +false+)</i>
# if true, any A and a is complemented into u and U; otherwise
# it is so, only if an U is found; otherwise DNA is assumed
#
# @raise [RuntimeError] if not +tolerant+ and chars are found for which
# no Watson-Crick complement is defined
# @raise [RuntimeError] if sequence contains both U and T
#
# @example
# "ACTG".rc # => "CAGT"
# "acGT".rc # => "ACgt"
# @example Undefined sequence is represented by "*":
# "*".rc # => "*"
# @example Extended IUPAC Alphabet:
# "ARBN".rc # => "NVYT"
# @example Usage with RNA sequences:
# "ACUG".rc # => "CAGU"
# "ACG".rc(rnasequence: true) # => "CGU"
# "ACUT".rc # (raises RuntimeError, both U and T)
def rc(tolerant: false, rnasequence: false)
return "*" if self == "*"
retval = each_char.map do |c|
if c == "U" or c == "u"
rnasequence = true
elsif rnasequence and (c == "T" or c == "t")
raise "String contains both U/u and T/t"
end
wcc = WCC.fetch(c, tolerant ? c : nil)
raise "#{self}: no Watson-Crick complement for #{c}" if wcc.nil?
wcc
end.reverse.join
if rnasequence
retval.tr!("tT","uU")
end
retval
end
# Watson-Crick Complements
WCC = {"a"=>"t","t"=>"a","A"=>"T","T"=>"A",
"c"=>"g","g"=>"c","C"=>"G","G"=>"C",
"b"=>"v","B"=>"V","v"=>"b","V"=>"B",
"h"=>"d","H"=>"D","d"=>"h","D"=>"H",
"R"=>"Y","Y"=>"R","r"=>"y","y"=>"r",
"K"=>"M","M"=>"K","k"=>"m","m"=>"k",
"S"=>"S","s"=>"s","w"=>"w","W"=>"W",
"n"=>"n","N"=>"N","u"=>"a","U"=>"A",
"-"=>"-","."=>".","="=>"=",
" "=>"","\n"=>""}
end
class String
include RGFA::Sequence
end
|
