Package Bio :: Package motifs :: Module transfac :: Class Motif
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Class Motif

source code

object --+    
     Motif --+
object --+   |
         |   |
      dict --+

Store the information for one TRANSFAC motif.

This class inherits from the Bio.motifs.Motif base class, as well as from a Python dictionary. All motif information found by the parser is stored as attributes of the base class when possible; see the Bio.motifs.Motif base class for a description of these attributes. All other information associated with the motif is stored as (key, value) pairs in the dictionary, where the key is the two-letter fields as found in the TRANSFAC file. References are an exception: These are stored in the .references attribute.

These fields are commonly found in TRANSFAC files:

AC:    Accession number
AS:    Accession numbers, secondary
BA:    Statistical basis
BF:    Binding factors
BS:    Factor binding sites underlying the matrix
       [sequence; SITE accession number; start position for matrix
       sequence; length of sequence used; number of gaps inserted;
       strand orientation.]
CC:    Comments
CO:    Copyright notice
DE:    Short factor description
DR:    External databases
       [database name: database accession number]
DT:    Date created/updated
HC:    Subfamilies
HP:    Superfamilies
ID:    Identifier
NA:    Name of the binding factor
OC:    Taxonomic classification
OS:    Species/Taxon
OV:    Older version
PV:    Preferred version
TY:    Type
XX:    Empty line; these are not stored in the Record.

References are stored in an .references attribute, which is a list of dictionaries with the following keys:

RN:    Reference number
RA:    Reference authors
RL:    Reference data
RT:    Reference title
RX:    PubMed ID

For more information, see the TRANSFAC documentation.

Instance Methods [hide private]

Inherited from Motif: __init__, __len__, __str__, format, reverse_complement, weblogo

Inherited from dict: __cmp__, __contains__, __delitem__, __eq__, __ge__, __getattribute__, __getitem__, __gt__, __iter__, __le__, __lt__, __ne__, __new__, __repr__, __setitem__, __sizeof__, clear, copy, fromkeys, get, has_key, items, iteritems, iterkeys, itervalues, keys, pop, popitem, setdefault, update, values, viewitems, viewkeys, viewvalues

Inherited from object: __delattr__, __format__, __reduce__, __reduce_ex__, __setattr__, __subclasshook__

Class Variables [hide private]
  multiple_value_keys = set(['BF', 'BS', 'DR', 'DT', 'HC', 'HP',...
  reference_keys = set(['RA', 'RL', 'RT', 'RX'])

Inherited from dict: __hash__

Properties [hide private]

Inherited from Motif: anticonsensus, background, consensus, degenerate_consensus, mask, pseudocounts, pssm, pwm

Inherited from object: __class__

Class Variable Details [hide private]


set(['BF', 'BS', 'DR', 'DT', 'HC', 'HP', 'OV'])