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Bio::KEGG::PATHWAY

Description

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

References

Constants

DELIMITER
TAGSIZE

Public Class Methods

new(entry) click to toggle source

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


Arguments:

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

Returns

Bio::KEGG::PATHWAY object

# File lib/bio/db/kegg/pathway.rb, line 72
def initialize(entry)
  super(entry, TAGSIZE)
end

Public Instance Methods

compounds() click to toggle source
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/pathway.rb, line 212
def compounds_as_hash
  unless @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/pathway.rb, line 205
def compounds_as_strings
  lines_fetch('COMPOUND')
end
definition() click to toggle source
Alias for: description
description() click to toggle source

Description of the pathway, described in the DESCRIPTION line.


Returns

String

# File lib/bio/db/kegg/pathway.rb, line 93
def description
  field_fetch('DESCRIPTION')
end
Also aliased as: definition
diseases() click to toggle source
Alias for: diseases_as_hash
diseases_as_hash() click to toggle source

Diseases described in the DISEASE lines.


Returns

Hash of disease ID and its definition

# File lib/bio/db/kegg/pathway.rb, line 129
def diseases_as_hash
  unless @diseases_as_hash
    @diseases_as_hash = strings_as_hash(diseases_as_strings)
  end
  @diseases_as_hash
end
Also aliased as: diseases
diseases_as_strings() click to toggle source

Disease described in the DISEASE lines.


Returns

Array containing String

# File lib/bio/db/kegg/pathway.rb, line 122
def diseases_as_strings
  lines_fetch('DISEASE')
end
entry_id() click to toggle source

Return the ID of the pathway, described in the ENTRY line.


Returns

String

# File lib/bio/db/kegg/pathway.rb, line 79
def entry_id
  field_fetch('ENTRY')[/\S+/]
end
enzymes() click to toggle source
Alias for: enzymes_as_strings
enzymes_as_strings() click to toggle source

Enzymes described in the ENZYME lines.


Returns

Array containing String

# File lib/bio/db/kegg/pathway.rb, line 179
def enzymes_as_strings
  lines_fetch('ENZYME')
end
Also aliased as: enzymes
genes() click to toggle source
Alias for: genes_as_hash
genes_as_hash() click to toggle source

Genes described in the GENE lines.


Returns

Hash of gene ID and its definition

# File lib/bio/db/kegg/pathway.rb, line 168
def genes_as_hash
  unless @genes_as_hash
    @genes_as_hash = strings_as_hash(genes_as_strings)
  end
  @genes_as_hash
end
Also aliased as: genes
genes_as_strings() click to toggle source

Genes described in the GENE lines.


Returns

Array containing String

# File lib/bio/db/kegg/pathway.rb, line 161
def genes_as_strings
  lines_fetch('GENE')
end
keggclass() click to toggle source

Return the name of the KEGG class, described in the CLASS line.


Returns

String

# File lib/bio/db/kegg/pathway.rb, line 101
def keggclass
  field_fetch('CLASS')
end
ko_pathway() click to toggle source

KO pathway described in the KO_PATHWAY line.


Returns

String

# File lib/bio/db/kegg/pathway.rb, line 247
def ko_pathway
  field_fetch('KO_PATHWAY')
end
modules() click to toggle source
Alias for: modules_as_hash
modules_as_hash() click to toggle source

Returns MODULE field as a Hash. Each key of the hash is KEGG MODULE ID, and each value is the name of the Pathway Module.


Returns

Hash

# File lib/bio/db/kegg/pathway.rb, line 59
def modules_as_hash; super; end
Also aliased as: modules
modules_as_strings() click to toggle source

Returns MODULE field of the entry.


Returns

Array containing String objects

# File lib/bio/db/kegg/pathway.rb, line 115
def modules_as_strings
  lines_fetch('MODULE')
end
name() click to toggle source

Name of the pathway, described in the NAME line.


Returns

String

# File lib/bio/db/kegg/pathway.rb, line 86
def name
  field_fetch('NAME')
end
organism() click to toggle source

Organism described in the ORGANISM line.


Returns

String

# File lib/bio/db/kegg/pathway.rb, line 154
def organism
  field_fetch('ORGANISM')
end
orthologs() click to toggle source
Alias for: orthologs_as_hash
orthologs_as_hash() click to toggle source

Returns a Hash of the orthology ID and definition in ORTHOLOGY field.

# File lib/bio/db/kegg/pathway.rb, line 43
def orthologs_as_hash; super; 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/pathway.rb, line 147
def orthologs_as_strings
  lines_fetch('ORTHOLOGY')
end
pathways() click to toggle source
Alias for: pathways_as_hash
pathways_as_hash() click to toggle source

Returns a Hash of the pathway ID and name in PATHWAY field.

# File lib/bio/db/kegg/pathway.rb, line 38
def pathways_as_hash; super; end
Also aliased as: pathways
pathways_as_strings() click to toggle source

Pathways described in the PATHWAY_MAP lines.


Returns

Array containing String

# File lib/bio/db/kegg/pathway.rb, line 108
def pathways_as_strings
  lines_fetch('PATHWAY_MAP')
end
reactions() click to toggle source
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/pathway.rb, line 194
def reactions_as_hash
  unless @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/pathway.rb, line 187
def reactions_as_strings
  lines_fetch('REACTION')
end
references() click to toggle source

REFERENCE – Returns contents of the REFERENCE records as an Array of Bio::Reference objects.


Returns

an Array containing Bio::Reference objects

# File lib/bio/db/kegg/pathway.rb, line 51
def references; super; end
rel_pathways() click to toggle source
rel_pathways_as_hash() click to toggle source

Returns REL_PATHWAY field as a Hash. Each key of the hash is Pathway ID, and each value is the name of the pathway.


Returns

Hash

# File lib/bio/db/kegg/pathway.rb, line 231
def rel_pathways_as_hash
  unless defined? @rel_pathways_as_hash then
    hash = {}
    rel_pathways_as_strings.each do |line|
      entry_id, name = line.split(/\s+/, 2)
      hash[entry_id] = name
    end
    @rel_pathways_as_hash = hash
  end
  @rel_pathways_as_hash
end
Also aliased as: rel_pathways
rel_pathways_as_strings() click to toggle source

Returns REL_PATHWAY field of the entry.


Returns

Array containing String objects

# File lib/bio/db/kegg/pathway.rb, line 223
def rel_pathways_as_strings
  lines_fetch('REL_PATHWAY')
end

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