Class: Bio::TRANSFAC

Inherits:
EMBLDB show all
Defined in:
lib/bio/db/transfac.rb

Direct Known Subclasses

CELL, CLASS, FACTOR, GENE, MATRIX, SITE

Defined Under Namespace

Classes: CELL, CLASS, FACTOR, GENE, MATRIX, SITE

Constant Summary collapse

DELIMITER = 
RS = "\n//\n"
TAGSIZE = 
4

Instance Method Summary collapse

Methods inherited from DB

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

Constructor Details

#initialize(entry) ⇒ TRANSFAC

Returns a new instance of TRANSFAC.



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# File 'lib/bio/db/transfac.rb', line 21

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

Instance Method Details

#ac ⇒ Object Also known as: entry_id

AC Accession number (1 per entry)

AC T00001 in the case of FACTOR AC M00001 in the case of MATRIX AC R00001 in the case of SITE AC G000001 in the case of GENE AC C00001 in the case of CLASS AC 00001 in the case of CELL



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# File 'lib/bio/db/transfac.rb', line 34

def ac
  unless @data['AC']
    @data['AC'] = fetch('AC')
  end
  @data['AC']
end

#cc ⇒ Object Also known as: comment 



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# File 'lib/bio/db/transfac.rb', line 52

def cc
  field_fetch('CC')
end

#dt ⇒ Object Also known as: date

DT Date (1 per entry)

DT DD.MM.YYYY (created); ewi. DT DD.MM.YYYY (updated); mpr.



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

def dt
  field_fetch('DT')
end

#oc ⇒ Object Also known as: org_class 



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

def oc
  field_fetch('OC')
end

#os ⇒ Object Also known as: org_species 



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# File 'lib/bio/db/transfac.rb', line 57

def os
  field_fetch('OS')
end

#ra ⇒ Object Also known as: ref_authors 



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

def ra
  field_fetch('RA')
end

#rl ⇒ Object Also known as: ref_data 



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# File 'lib/bio/db/transfac.rb', line 82

def rl
  field_fetch('RL')
end

#rn ⇒ Object Also known as: ref_no 



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# File 'lib/bio/db/transfac.rb', line 67

def rn
  field_fetch('RN')
end

#rt ⇒ Object Also known as: ref_title 



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# File 'lib/bio/db/transfac.rb', line 77

def rt
  field_fetch('RT')
end