Package Bio :: Package motifs :: Module transfac :: Class Motif
[hide private]
[frames] | no frames]

Class Motif

source code

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

A Bio.motifs.transfac.Motif stores the information in 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]

multiple_value_keys

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