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
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
|
#
# = bio/db/kegg/module.rb - KEGG MODULE database class
#
# Copyright:: Copyright (C) 2010 Kozo Nishida <kozo-ni@is.naist.jp>
# Copyright:: Copyright (C) 2010 Toshiaki Katayama <k@bioruby.org>
# License:: The Ruby License
#
#
require 'bio/db'
require 'bio/db/kegg/common'
module Bio
class KEGG
# == Description
#
# Bio::KEGG::MODULE is a parser class for the KEGG MODULE database entry.
#
# == References
#
# * http://www.kegg.jp/kegg-bin/get_htext?ko00002.keg
# * ftp://ftp.genome.jp/pub/kegg/pathway/module
#
class MODULE < KEGGDB
DELIMITER = RS = "\n///\n"
TAGSIZE = 12
#--
# for a private method strings_as_hash.
#++
include Common::StringsAsHash
# Creates a new Bio::KEGG::MODULE object.
# ---
# *Arguments*:
# * (required) _entry_: (String) single entry as a string
# *Returns*:: Bio::KEGG::MODULE object
def initialize(entry)
super(entry, TAGSIZE)
end
# Return the ID, described in the ENTRY line.
# ---
# *Returns*:: String
def entry_id
field_fetch('ENTRY')[/\S+/]
end
# Name of the module, described in the NAME line.
# ---
# *Returns*:: String
def name
field_fetch('NAME')
end
# Definition of the module, described in the DEFINITION line.
# ---
# *Returns*:: String
def definition
field_fetch('DEFINITION')
end
# Name of the KEGG class, described in the CLASS line.
# ---
# *Returns*:: String
def keggclass
field_fetch('CLASS')
end
# Pathways described in the PATHWAY lines.
# ---
# *Returns*:: Array containing String
def pathways_as_strings
lines_fetch('PATHWAY')
end
# Pathways described in the PATHWAY lines.
# ---
# *Returns*:: Hash of pathway ID and its definition
def pathways_as_hash
unless (defined? @pathways_as_hash) && @pathways_as_hash
@pathways_as_hash = strings_as_hash(pathways_as_strings)
end
@pathways_as_hash
end
alias pathways pathways_as_hash
# Orthologs described in the ORTHOLOGY lines.
# ---
# *Returns*:: Array containing String
def orthologs_as_strings
lines_fetch('ORTHOLOGY')
end
# Orthologs described in the ORTHOLOGY lines.
# ---
# *Returns*:: Hash of orthology ID and its definition
def orthologs_as_hash
unless (defined? @orthologs_as_hash) && @orthologs_as_hash
@orthologs_as_hash = strings_as_hash(orthologs_as_strings)
end
@orthologs_as_hash
end
alias orthologs orthologs_as_hash
# All KO IDs in the ORTHOLOGY lines.
# ---
# *Returns*:: Array of orthology IDs
def orthologs_as_array
orthologs_as_hash.keys.map{|x| x.split(/\+|\-|,/)}.flatten.sort.uniq
end
# Reactions described in the REACTION lines.
# ---
# *Returns*:: Array containing String
def reactions_as_strings
lines_fetch('REACTION')
end
# Reactions described in the REACTION lines.
# ---
# *Returns*:: Hash of reaction ID and its definition
def reactions_as_hash
unless (defined? @reactions_as_hash) && @reactions_as_hash
@reactions_as_hash = strings_as_hash(reactions_as_strings)
end
@reactions_as_hash
end
alias reactions reactions_as_hash
# Compounds described in the COMPOUND lines.
# ---
# *Returns*:: Array containing String
def compounds_as_strings
lines_fetch('COMPOUND')
end
# Compounds described in the COMPOUND lines.
# ---
# *Returns*:: Hash of compound ID and its definition
def compounds_as_hash
unless (defined? @compounds_as_hash) && @compounds_as_hash
@compounds_as_hash = strings_as_hash(compounds_as_strings)
end
@compounds_as_hash
end
alias compounds compounds_as_hash
end # MODULE
end # KEGG
end # Bio
|
