Class: Bio::KEGG::MODULE

Inherits:
Bio::KEGGDB show all
Includes:
Common::StringsAsHash
Defined in:
lib/bio/db/kegg/module.rb

Overview

Description

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

References

Constant Summary collapse

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

Instance Method Summary collapse

Methods inherited from DB

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

Constructor Details

#initialize(entry) ⇒ MODULE

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


Arguments:

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

Returns

Bio::KEGG::MODULE object


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# File 'lib/bio/db/kegg/module.rb', line 40

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/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

#compounds_as_stringsObject

Compounds described in the COMPOUND lines.


Returns

Array containing String


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# File 'lib/bio/db/kegg/module.rb', line 139

def compounds_as_strings
  lines_fetch('COMPOUND')
end

#definitionObject

Definition of the module, described in the DEFINITION line.


Returns

String


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# File 'lib/bio/db/kegg/module.rb', line 61

def definition
  field_fetch('DEFINITION')
end

#entry_idObject

Return the ID, described in the ENTRY line.


Returns

String


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# File 'lib/bio/db/kegg/module.rb', line 47

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

#keggclassObject

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


Returns

String


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# File 'lib/bio/db/kegg/module.rb', line 68

def keggclass
  field_fetch('CLASS')
end

#nameObject

Name of the module, described in the NAME line.


Returns

String


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# File 'lib/bio/db/kegg/module.rb', line 54

def name
  field_fetch('NAME')
end

#orthologs_as_arrayObject

All KO IDs in the ORTHOLOGY lines.


Returns

Array of orthology IDs


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# 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_hashObject Also known as: orthologs

Orthologs described in the ORTHOLOGY lines.


Returns

Hash of orthology ID and its definition


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# 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

#orthologs_as_stringsObject

Orthologs described in the ORTHOLOGY lines.


Returns

Array containing String


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# File 'lib/bio/db/kegg/module.rb', line 94

def orthologs_as_strings
  lines_fetch('ORTHOLOGY')
end

#pathways_as_hashObject Also known as: pathways

Pathways described in the PATHWAY lines.


Returns

Hash of pathway ID and its definition


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# 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

#pathways_as_stringsObject

Pathways described in the PATHWAY lines.


Returns

Array containing String


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# File 'lib/bio/db/kegg/module.rb', line 75

def pathways_as_strings
  lines_fetch('PATHWAY')
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/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

#reactions_as_stringsObject

Reactions described in the REACTION lines.


Returns

Array containing String


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# File 'lib/bio/db/kegg/module.rb', line 120

def reactions_as_strings
  lines_fetch('REACTION')
end