Class: Bio::KEGG::PATHWAY

Overview

Description

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

References

Constant Summary

DELIMITER =
RS = "\n///\n"
TAGSIZE =
12

Instance Method Summary collapse

Methods inherited from DB

#exists?, #fetch, #get, open, #tags

Constructor Details

#initialize(entry) ⇒ PATHWAY

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


Arguments:

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

Returns

Bio::KEGG::PATHWAY object



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# File 'lib/bio/db/kegg/pathway.rb', line 72

def initialize(entry)
  super(entry, TAGSIZE)
end

Instance Method Details

#compounds_as_hashObject Also known as: compounds

Compounds described in the COMPOUND lines.


Returns

Hash of compound ID and its definition



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# 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

#compounds_as_stringsObject

Compounds described in the COMPOUND lines.


Returns

Array containing String



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# File 'lib/bio/db/kegg/pathway.rb', line 205

def compounds_as_strings
  lines_fetch('COMPOUND')
end


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# File 'lib/bio/db/kegg/pathway.rb', line 33

def dblinks_as_hash; super; end

Returns an Array of a database name and entry IDs in DBLINKS field.


Returns

Array containing String



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# File 'lib/bio/db/kegg/pathway.rb', line 140

def dblinks_as_strings
  lines_fetch('DBLINKS')
end

#descriptionObject Also known as: definition

Description of the pathway, described in the DESCRIPTION line.


Returns

String



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# File 'lib/bio/db/kegg/pathway.rb', line 93

def description
  field_fetch('DESCRIPTION')
end

#diseases_as_hashObject Also known as: diseases

Diseases described in the DISEASE lines.


Returns

Hash of disease ID and its definition



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# 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

#diseases_as_stringsObject

Disease described in the DISEASE lines.


Returns

Array containing String



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# File 'lib/bio/db/kegg/pathway.rb', line 122

def diseases_as_strings
  lines_fetch('DISEASE')
end

#entry_idObject

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


Returns

String



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# File 'lib/bio/db/kegg/pathway.rb', line 79

def entry_id
  field_fetch('ENTRY')[/\S+/]
end

#enzymes_as_stringsObject Also known as: enzymes

Enzymes described in the ENZYME lines.


Returns

Array containing String



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# File 'lib/bio/db/kegg/pathway.rb', line 179

def enzymes_as_strings
  lines_fetch('ENZYME')
end

#genes_as_hashObject Also known as: genes

Genes described in the GENE lines.


Returns

Hash of gene ID and its definition



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# 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

#genes_as_stringsObject

Genes described in the GENE lines.


Returns

Array containing String



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# File 'lib/bio/db/kegg/pathway.rb', line 161

def genes_as_strings
  lines_fetch('GENE')
end

#keggclassObject

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


Returns

String



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# File 'lib/bio/db/kegg/pathway.rb', line 101

def keggclass
  field_fetch('CLASS')
end

#ko_pathwayObject

KO pathway described in the KO_PATHWAY line.


Returns

String



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# File 'lib/bio/db/kegg/pathway.rb', line 247

def ko_pathway
  field_fetch('KO_PATHWAY')
end

#modules_as_hashObject Also known as: modules



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# File 'lib/bio/db/kegg/pathway.rb', line 59

def modules_as_hash; super; end

#modules_as_stringsObject

Returns MODULE field of the entry.


Returns

Array containing String objects



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# File 'lib/bio/db/kegg/pathway.rb', line 115

def modules_as_strings
  lines_fetch('MODULE')
end

#nameObject

Name of the pathway, described in the NAME line.


Returns

String



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# File 'lib/bio/db/kegg/pathway.rb', line 86

def name
  field_fetch('NAME')
end

#organismObject

Organism described in the ORGANISM line.


Returns

String



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# File 'lib/bio/db/kegg/pathway.rb', line 154

def organism
  field_fetch('ORGANISM')
end

#orthologs_as_hashObject Also known as: orthologs



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# File 'lib/bio/db/kegg/pathway.rb', line 43

def orthologs_as_hash; super; end

#orthologs_as_stringsObject

Orthologs described in the ORTHOLOGY lines.


Returns

Array containing String



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# File 'lib/bio/db/kegg/pathway.rb', line 147

def orthologs_as_strings
  lines_fetch('ORTHOLOGY')
end

#pathways_as_hashObject Also known as: pathways



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# File 'lib/bio/db/kegg/pathway.rb', line 38

def pathways_as_hash; super; end

#pathways_as_stringsObject

Pathways described in the PATHWAY_MAP lines.


Returns

Array containing String



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# File 'lib/bio/db/kegg/pathway.rb', line 108

def pathways_as_strings
  lines_fetch('PATHWAY_MAP')
end

#reactions_as_hashObject Also known as: reactions

Reactions described in the REACTION lines.


Returns

Hash of reaction ID and its definition



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# 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

#reactions_as_stringsObject

Reactions described in the REACTION lines.


Returns

Array containing String



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# File 'lib/bio/db/kegg/pathway.rb', line 187

def reactions_as_strings
  lines_fetch('REACTION')
end

#referencesObject



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# File 'lib/bio/db/kegg/pathway.rb', line 51

def references; super; end

#rel_pathways_as_hashObject Also known as: rel_pathways

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



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# 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

#rel_pathways_as_stringsObject

Returns REL_PATHWAY field of the entry.


Returns

Array containing String objects



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# File 'lib/bio/db/kegg/pathway.rb', line 223

def rel_pathways_as_strings
  lines_fetch('REL_PATHWAY')
end