# Bio.motifs.transfac module

Parsing TRANSFAC files.

class Bio.motifs.transfac.Motif(alphabet='ACGT', alignment=None, counts=None)

  Bases: `Motif`, `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.

  multiple_value_keys = {'BF', 'BS', 'CC', 'DR', 'DT', 'HC', 'HP', 'OV'}
  reference_keys = {'RA', 'RL', 'RT', 'RX'}
  __getitem__(key)

    Return a new Motif object for the positions included in key.

        >>> from Bio import motifs
        >>> motif = motifs.create(["AACGCCA", "ACCGCCC", "AACTCCG"])
        >>> print(motif)
        AACGCCA
        ACCGCCC
        AACTCCG
        >>> print(motif[:-1])
        AACGCC
        ACCGCC
        AACTCC

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 13
  __static_attributes__ = ()

class Bio.motifs.transfac.Record

  Bases: `list`

  Store the information in a TRANSFAC matrix table.

  The record inherits from a list containing the individual motifs.

  Attributes:

    - version - The version number, corresponding to the ‘VV’ field in the TRANSFAC file;

  __init__()

    Initialize the class.

  __str__()

    Turn the TRANSFAC matrix into a string.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 78
  __static_attributes__ = ('version',)

Bio.motifs.transfac.read(handle, strict=True)

  Parse a transfac format handle into a Record object.

Bio.motifs.transfac.write(motifs)

  Write the representation of a motif in TRANSFAC format.

Biopython v: 1.86

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