class Bio::KEGG::MODULE

Description

Bio::KEGG::MODULE is a parser class for the KEGG MODULE database entry.

References

Constants

DELIMITER
TAGSIZE

Public Class Methods

new(entry) click to toggle source

Creates a new Bio::KEGG::MODULE object.


Arguments:

  • (required) entry: (String) single entry as a string

Returns

Bio::KEGG::MODULE object

Calls superclass method Bio::NCBIDB.new
# File lib/bio/db/kegg/module.rb, line 40
def initialize(entry)
  super(entry, TAGSIZE)
end

Public Instance Methods

compounds()
Alias for: compounds_as_hash
compounds_as_hash() click to toggle source

Compounds described in the COMPOUND lines.


Returns

Hash of compound ID and its definition

# File lib/bio/db/kegg/module.rb, line 146
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
Also aliased as: compounds
compounds_as_strings() click to toggle source

Compounds described in the COMPOUND lines.


Returns

Array containing String

# File lib/bio/db/kegg/module.rb, line 139
def compounds_as_strings
  lines_fetch('COMPOUND')
end
definition() click to toggle source

Definition of the module, described in the DEFINITION line.


Returns

String

# File lib/bio/db/kegg/module.rb, line 61
def definition
  field_fetch('DEFINITION')
end
entry_id() click to toggle source

Return the ID, described in the ENTRY line.


Returns

String

# File lib/bio/db/kegg/module.rb, line 47
def entry_id
  field_fetch('ENTRY')[/\S+/]
end
keggclass() click to toggle source

Name of the KEGG class, described in the CLASS line.


Returns

String

# File lib/bio/db/kegg/module.rb, line 68
def keggclass
  field_fetch('CLASS')
end
name() click to toggle source

Name of the module, described in the NAME line.


Returns

String

# File lib/bio/db/kegg/module.rb, line 54
def name
  field_fetch('NAME')
end
orthologs()
Alias for: orthologs_as_hash
orthologs_as_array() click to toggle source

All KO IDs in the ORTHOLOGY lines.


Returns

Array of orthology IDs

# File lib/bio/db/kegg/module.rb, line 112
def orthologs_as_array
  orthologs_as_hash.keys.map{|x| x.split(/\+|\-|,/)}.flatten.sort.uniq
end
orthologs_as_hash() click to toggle source

Orthologs described in the ORTHOLOGY lines.


Returns

Hash of orthology ID and its definition

# File lib/bio/db/kegg/module.rb, line 101
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
Also aliased as: orthologs
orthologs_as_strings() click to toggle source

Orthologs described in the ORTHOLOGY lines.


Returns

Array containing String

# File lib/bio/db/kegg/module.rb, line 94
def orthologs_as_strings
  lines_fetch('ORTHOLOGY')
end
pathways()
Alias for: pathways_as_hash
pathways_as_hash() click to toggle source

Pathways described in the PATHWAY lines.


Returns

Hash of pathway ID and its definition

# File lib/bio/db/kegg/module.rb, line 82
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
Also aliased as: pathways
pathways_as_strings() click to toggle source

Pathways described in the PATHWAY lines.


Returns

Array containing String

# File lib/bio/db/kegg/module.rb, line 75
def pathways_as_strings
  lines_fetch('PATHWAY')
end
reactions()
Alias for: reactions_as_hash
reactions_as_hash() click to toggle source

Reactions described in the REACTION lines.


Returns

Hash of reaction ID and its definition

# File lib/bio/db/kegg/module.rb, line 127
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
Also aliased as: reactions
reactions_as_strings() click to toggle source

Reactions described in the REACTION lines.


Returns

Array containing String

# File lib/bio/db/kegg/module.rb, line 120
def reactions_as_strings
  lines_fetch('REACTION')
end