Class: Bio::KEGG::MODULE

Inherits:

Bio::KEGGDB

• Object
• DB
• NCBIDB
• Bio::KEGGDB
• Bio::KEGG::MODULE

show all

Includes:

Common::StringsAsHash

Defined in:

lib/bio/db/kegg/module.rb

Overview

Constant Summary

DELIMITER =

RS = "\n///\n"

TAGSIZE =

12

Instance Method Summary (collapse)

• - (Object) compounds_as_hash (also: #compounds)

  Compounds described in the COMPOUND lines.

• - (Object) compounds_as_strings

  Compounds described in the COMPOUND lines.

• - (Object) definition

  Definition of the module, described in the DEFINITION line.

• - (Object) entry_id

  Return the ID, described in the ENTRY line.

• - (MODULE) initialize(entry) constructor

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

• - (Object) keggclass

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

• - (Object) name

  Name of the module, described in the NAME line.

• - (Object) orthologs_as_array

  All KO IDs in the ORTHOLOGY lines.

• - (Object) orthologs_as_hash (also: #orthologs)

  Orthologs described in the ORTHOLOGY lines.

• - (Object) orthologs_as_strings

  Orthologs described in the ORTHOLOGY lines.

• - (Object) pathways_as_hash (also: #pathways)

  Pathways described in the PATHWAY lines.

• - (Object) pathways_as_strings

  Pathways described in the PATHWAY lines.

• - (Object) reactions_as_hash (also: #reactions)

  Reactions described in the REACTION lines.

• - (Object) reactions_as_strings

  Reactions described in the REACTION lines.

Methods inherited from DB

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

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# File 'lib/bio/db/kegg/module.rb', line 41

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

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

def compounds_as_hash
  unless @compounds_as_hash
    @compounds_as_hash = strings_as_hash(compounds_as_strings)
  end
  @compounds_as_hash
end

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

def compounds_as_strings
  lines_fetch('COMPOUND')
end

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# File 'lib/bio/db/kegg/module.rb', line 62

def definition
  field_fetch('DEFINITION')
end

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# File 'lib/bio/db/kegg/module.rb', line 48

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

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# File 'lib/bio/db/kegg/module.rb', line 69

def keggclass
  field_fetch('CLASS')
end

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# File 'lib/bio/db/kegg/module.rb', line 55

def name
  field_fetch('NAME')
end

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# File 'lib/bio/db/kegg/module.rb', line 113

def orthologs_as_array
  orthologs_as_hash.keys.map{|x| x.split(/\+|\-|,/)}.flatten.sort.uniq
end

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# File 'lib/bio/db/kegg/module.rb', line 102

def orthologs_as_hash
  unless @orthologs_as_hash
    @orthologs_as_hash = strings_as_hash(orthologs_as_strings)
  end
  @orthologs_as_hash
end

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# File 'lib/bio/db/kegg/module.rb', line 95

def orthologs_as_strings
  lines_fetch('ORTHOLOGY')
end

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# File 'lib/bio/db/kegg/module.rb', line 83

def pathways_as_hash
  unless @pathways_as_hash
    @pathways_as_hash = strings_as_hash(pathways_as_strings)
  end
  @pathways_as_hash
end

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# File 'lib/bio/db/kegg/module.rb', line 76

def pathways_as_strings
  lines_fetch('PATHWAY')
end

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# File 'lib/bio/db/kegg/module.rb', line 128

def reactions_as_hash
  unless @reactions_as_hash
    @reactions_as_hash = strings_as_hash(reactions_as_strings)
  end
  @reactions_as_hash
end

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# File 'lib/bio/db/kegg/module.rb', line 121

def reactions_as_strings
  lines_fetch('REACTION')
end