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| # Copyright 2015 by Gert Hulselmans. All rights reserved. | |
| # This file is part of the Biopython distribution and governed by your | |
| # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". | |
| # Please see the LICENSE file that should have been included as part of this | |
| # package. | |
| """Parse XMS motif files.""" | |
| from Bio import motifs | |
| from xml.dom import minidom, Node | |
| import re | |
| class XMSScanner: | |
| """Class for scanning XMS XML file.""" | |
| def __init__(self, doc): | |
| """Generate motif Record from xms document, an XML-like motif pfm file.""" | |
| self.record = Record() | |
| for child in doc.getElementsByTagName("motif"): | |
| if child.nodeType == Node.ELEMENT_NODE: | |
| self.handle_motif(child) | |
| def handle_motif(self, node): | |
| """Read the motif's name and column from the node and add the motif record.""" | |
| motif_name = self.get_text(node.getElementsByTagName("name")) | |
| nucleotide_counts = {"A": [], "C": [], "G": [], "T": []} | |
| for column in node.getElementsByTagName("column"): | |
| [ | |
| nucleotide_counts[nucleotide].append(float(nucleotide_count)) | |
| for nucleotide, nucleotide_count in zip( | |
| ["A", "C", "G", "T"], self.get_acgt(column) | |
| ) | |
| ] | |
| motif = motifs.Motif(alphabet="GATC", counts=nucleotide_counts) | |
| motif.name = motif_name | |
| self.record.append(motif) | |
| def get_property_value(self, node, key_name): | |
| """Extract the value of the motif's property named key_name from node.""" | |
| for cur_property in node.getElementsByTagName("prop"): | |
| right_property = False | |
| cur_value = None | |
| for child in cur_property.childNodes: | |
| if child.nodeType != Node.ELEMENT_NODE: | |
| continue | |
| if child.tagName == "key" and self.get_text([child]) == key_name: | |
| right_property = True | |
| if child.tagName == "value": | |
| cur_value = self.get_text([child]) | |
| if right_property: | |
| return cur_value | |
| return None | |
| def get_acgt(self, node): | |
| """Get and return the motif's weights of A, C, G, T.""" | |
| a, c, g, t = 0.0, 0.0, 0.0, 0.0 | |
| for weight in node.getElementsByTagName("weight"): | |
| if weight.getAttribute("symbol") == "adenine": | |
| a = float(self.get_text([weight])) | |
| elif weight.getAttribute("symbol") == "cytosine": | |
| c = float(self.get_text([weight])) | |
| elif weight.getAttribute("symbol") == "guanine": | |
| g = float(self.get_text([weight])) | |
| elif weight.getAttribute("symbol") == "thymine": | |
| t = float(self.get_text([weight])) | |
| return a, c, g, t | |
| def get_text(self, nodelist): | |
| """Return a string representation of the motif's properties listed on nodelist .""" | |
| retlist = [] | |
| for node in nodelist: | |
| if node.nodeType == Node.TEXT_NODE: | |
| retlist.append(node.wholeText) | |
| elif node.hasChildNodes: | |
| retlist.append(self.get_text(node.childNodes)) | |
| return re.sub(r"\s+", " ", "".join(retlist)) | |
| class Record(list): | |
| """Class to store the information in a XMS matrix table. | |
| The record inherits from a list containing the individual motifs. | |
| """ | |
| def __str__(self): | |
| """Return a string representation of the motifs in the Record object.""" | |
| return "\n".join(str(motif) for motif in self) | |
| def 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. | |
| """ | |
| xms_doc = minidom.parse(handle) | |
| record = XMSScanner(xms_doc).record | |
| return record | |