Bio.motifs.xms module¶
Parse XMS motif files.
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class
Bio.motifs.xms.
XMSScanner
(doc)¶ Bases:
object
Class for scanning XMS XML file.
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__init__
(self, doc)¶ Generate motif Record from xms document, an XML-like motif pfm file.
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handle_motif
(self, node)¶ Read the motif’s name and column from the node and add the motif record.
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get_property_value
(self, node, key_name)¶ Extract the value of the motif’s property named key_name from node.
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get_acgt
(self, node)¶ Get and return the motif’s weights of A, C, G, T.
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get_text
(self, nodelist)¶ Return a string representation of the motif’s properties listed on nodelist .
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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.
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__str__
(self)¶ Return str(self).
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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.