class Bio::KEGG::Keggtab
Description¶ ↑
Parse ‘keggtab’ KEGG database definition file which also includes Taxonomic category of the KEGG organisms.
References¶ ↑
The ‘keggtab’ file is included in
Format¶ ↑
File format is something like
# KEGGTAB # # name type directory abbreviation # enzyme enzyme $BIOROOT/db/ideas/ligand ec ec alias enzyme (snip) # Human h.sapiens genes $BIOROOT/db/kegg/genes hsa H.sapiens alias h.sapiens hsa alias h.sapiens (snip) # # Taxonomy # (snip) animals alias hsa+mmu+rno+dre+dme+cel eukaryotes alias animals+plants+protists+fungi genes alias eubacteria+archaea+eukaryotes
Attributes
Returns a string of the BIOROOT path prefix.
Public Class Methods
Path for keggtab file and optionally set bioroot top directory. Environmental variable BIOROOT overrides bioroot.
# File lib/bio/db/kegg/keggtab.rb 54 def initialize(file_path, bioroot = nil) 55 @bioroot = ENV['BIOROOT'] || bioroot 56 @db_names = Hash.new 57 @database = Hash.new 58 @taxonomy = Hash.new 59 File.open(file_path) do |f| 60 parse_keggtab(f.read) 61 end 62 end
Public Instance Methods
deprecated
# File lib/bio/db/kegg/keggtab.rb 141 def alias_list(db_name) 142 if @db_names[db_name] 143 @db_names[db_name].aliases 144 end 145 end
Returns an Array containing all alias names for the database. (e.g. ‘hsa’ -> [“H.sapiens”, “hsa”], ‘hpj’ -> [“H.pylori_J99”, “hpj”])
# File lib/bio/db/kegg/keggtab.rb 112 def aliases(db_abbrev) 113 if @database[db_abbrev] 114 @database[db_abbrev].aliases 115 end 116 end
# File lib/bio/db/kegg/keggtab.rb 196 def child_nodes(node = 'genes') 197 return @taxonomy[node] 198 end
Returns a hash containing DB definition section of the keggtab file. If database name is given as an argument, returns a Keggtab::DB object.
# File lib/bio/db/kegg/keggtab.rb 102 def database(db_abbrev = nil) 103 if db_abbrev 104 @database[db_abbrev] 105 else 106 @database 107 end 108 end
deprecated
# File lib/bio/db/kegg/keggtab.rb 157 def db_by_abbrev(db_abbrev) 158 @db_names.each do |k, db| 159 return db if db.abbrev == db_abbrev 160 end 161 return nil 162 end
deprecated
# File lib/bio/db/kegg/keggtab.rb 148 def db_path(db_name) 149 if @bioroot 150 "#{@db_names[db_name].path.sub(/\$BIOROOT/,@bioroot)}/#{db_name}" 151 else 152 "#{@db_names[db_name].path}/#{db_name}" 153 end 154 end
deprecated
# File lib/bio/db/kegg/keggtab.rb 170 def db_path_by_abbrev(db_abbrev) 171 db_name = name_by_abbrev(db_abbrev) 172 db_path(db_name) 173 end
Returns an array of taxonomy names the organism belongs. (e.g. ‘eco’ -> [‘proteogamma’,‘proteobacteria’,‘eubacteria’,‘genes’]) This method has aliases as keggorg2taxo, korg2taxonomy, keggorg2taxonomy.
# File lib/bio/db/kegg/keggtab.rb 225 def korg2taxo(keggorg) 226 tmp = Array.new 227 traverse = Proc.new {|keggorg| 228 @taxonomy.each do |k,v| 229 if v.include?(keggorg) 230 tmp.push(k) 231 traverse.call(k) 232 break 233 end 234 end 235 } 236 traverse.call(keggorg) 237 return tmp 238 end
Returns a canonical database name for the abbreviation. (e.g. ‘ec’ -> ‘enzyme’, ‘hsa’ -> ‘h.sapies’, …)
# File lib/bio/db/kegg/keggtab.rb 120 def name(db_abbrev) 121 if @database[db_abbrev] 122 @database[db_abbrev].name 123 end 124 end
deprecated
# File lib/bio/db/kegg/keggtab.rb 165 def name_by_abbrev(db_abbrev) 166 db_by_abbrev(db_abbrev).name 167 end
Returns an absolute path for the flat file database. (e.g. ‘/bio/db/kegg/genes’, …)
# File lib/bio/db/kegg/keggtab.rb 128 def path(db_abbrev) 129 if @database[db_abbrev] 130 file = @database[db_abbrev].name 131 if @bioroot 132 "#{@database[db_abbrev].path.sub(/\$BIOROOT/,@bioroot)}/#{file}" 133 else 134 "#{@database[db_abbrev].path}/#{file}" 135 end 136 end 137 end
List of all node labels from Taxonomy section. (e.g. [“actinobacteria”, “animals”, “archaea”, “bacillales”, …)
# File lib/bio/db/kegg/keggtab.rb 192 def taxa_list 193 @taxonomy.keys.sort 194 end
Returns an array of organism names included in the specified taxon label. (e.g. ‘proteobeta’ -> [“nme”, “nma”, “rso”]) This method has taxo2keggorgs, taxon2korgs, and taxon2keggorgs aliases.
# File lib/bio/db/kegg/keggtab.rb 203 def taxo2korgs(node = 'genes') 204 if node.length == 3 205 return node 206 else 207 if @taxonomy[node] 208 tmp = Array.new 209 @taxonomy[node].each do |x| 210 tmp.push(taxo2korgs(x)) 211 end 212 return tmp 213 else 214 return nil 215 end 216 end 217 end
Returns a hash containing Taxonomy section of the keggtab file. If argument is given, returns a List of all child nodes belongs to the label node. (e.g. “eukaryotes” -> [“animals”, “plants”, “protists”, “fungi”], …)
# File lib/bio/db/kegg/keggtab.rb 182 def taxonomy(node = nil) 183 if node 184 @taxonomy[node] 185 else 186 @taxonomy 187 end 188 end