# Bio.motifs.xms module

Parse XMS motif files.

class Bio.motifs.xms.XMSScanner(doc)

  Bases: `object`

  Class for scanning XMS XML file.

  __init__(doc)

    Generate motif Record from xms document, an XML-like motif pfm file.

  handle_motif(node)

    Read the motif’s name and column from the node and add the motif record.

  get_property_value(node, key_name)

    Extract the value of the motif’s property named key_name from node.

  get_acgt(node)

    Get and return the motif’s weights of A, C, G, T.

  get_text(nodelist)

    Return a string representation of the motif’s properties listed on nodelist .

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 16
  __static_attributes__ = ('record',)

class Bio.motifs.xms.Record(iterable=(), /)

  Bases: `list`

  Class to store the information in a XMS matrix table.

  The record inherits from a list containing the individual motifs.

  __str__()

    Return a string representation of the motifs in the Record object.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 86
  __static_attributes__ = ()

Bio.motifs.xms.read(handle)

  Read motifs in XMS matrix format from a file handle.

  XMS is an XML format for describing regulatory motifs and PSSMs. This format was defined by Thomas Down, and used in the NestedMICA and MotifExplorer programs.

Biopython v: 1.86

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