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