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| # Copyright 2008 by Bartek Wilczynski. | |
| # Adapted from Bio.MEME.Parser by Jason A. Hackney. All rights reserved. | |
| # This code is part of the Biopython distribution and governed by its | |
| # license. Please see the LICENSE file that should have been included | |
| # as part of this package. | |
| """Module for the support of Motif Alignment and Search Tool (MAST).""" | |
| import xml.etree.ElementTree as ET | |
| from Bio.motifs import meme | |
| class Record(list): | |
| """The class for holding the results from a MAST run. | |
| A mast.Record holds data about matches between motifs and sequences. | |
| The motifs held by the Record are objects of the class meme.Motif. | |
| The mast.Record class inherits from list, so you can access individual | |
| motifs in the record by their index. Alternatively, you can find a motif | |
| by its name: | |
| >>> from Bio import motifs | |
| >>> with open("motifs/mast.crp0.de.oops.txt.xml") as f: | |
| ... record = motifs.parse(f, 'MAST') | |
| >>> motif = record[0] | |
| >>> print(motif.name) | |
| 1 | |
| >>> motif = record['1'] | |
| >>> print(motif.name) | |
| 1 | |
| """ | |
| def __init__(self): | |
| """Initialize the class.""" | |
| self.sequences = [] | |
| self.version = "" | |
| self.database = "" | |
| self.diagrams = {} | |
| self.alphabet = None | |
| self.strand_handling = "" | |
| def __getitem__(self, key): | |
| """Return the motif of index key.""" | |
| if isinstance(key, str): | |
| for motif in self: | |
| if motif.name == key: | |
| return motif | |
| else: | |
| return list.__getitem__(self, key) | |
| def read(handle): | |
| """Parse a MAST XML format handle as a Record object.""" | |
| record = Record() | |
| try: | |
| xml_tree = ET.parse(handle) | |
| except ET.ParseError: | |
| raise ValueError( | |
| "Improper MAST XML input file. XML root tag should start with <mast version= ..." | |
| ) | |
| __read_metadata(record, xml_tree) | |
| __read_sequences(record, xml_tree) | |
| return record | |
| # Everything below is private | |
| def __read_metadata(record, xml_tree): | |
| record.version = xml_tree.getroot().get("version") | |
| record.database = xml_tree.find("sequence_dbs").find("sequence_db").get("source") | |
| record.alphabet = xml_tree.find("alphabet").get("name") | |
| record.strand_handling = xml_tree.find("settings").get("strand_handling") | |
| # TODO - read other metadata | |
| for i, motif_tree in enumerate(xml_tree.find("motifs").findall("motif")): | |
| motif = meme.Motif(record.alphabet) | |
| # TODO - motif.name not in XML - always index? | |
| motif.name = str(i + 1) | |
| motif.id = motif_tree.get("id") | |
| motif.alt_id = motif_tree.get("alt") | |
| motif.length = int(motif_tree.get("length")) | |
| # TODO - add nsites, evalue | |
| record.append(motif) | |
| def __read_sequences(record, xml_tree): | |
| """Read sequences from XML ElementTree object.""" | |
| for sequence_tree in xml_tree.find("sequences").findall("sequence"): | |
| sequence_name = sequence_tree.get("name") | |
| record.sequences.append(sequence_name) | |
| diagram_str = __make_diagram(record, sequence_tree) | |
| record.diagrams[sequence_name] = diagram_str | |
| # TODO - add description, evalue, length, combined_pvalue | |
| def __make_diagram(record, sequence_tree): | |
| """Make diagram string found in text file based on motif hit info.""" | |
| sequence_length = int(sequence_tree.get("length")) | |
| hit_eles, hit_motifs, gaps = [], [], [] | |
| for seg_tree in sequence_tree.findall("seg"): | |
| for hit_ele in seg_tree.findall("hit"): | |
| hit_pos = int(hit_ele.get("pos")) | |
| if not hit_eles: | |
| gap = hit_pos - 1 | |
| else: | |
| gap = hit_pos - int(hit_eles[-1].get("pos")) - hit_motifs[-1].length | |
| gaps.append(gap) | |
| hit_motifs.append(record[int(hit_ele.get("idx"))]) | |
| hit_eles.append(hit_ele) | |
| if not hit_eles: | |
| return str(sequence_length) | |
| if record.strand_handling == "combine": | |
| motif_strs = [ | |
| f"[{'-' if hit_ele.get('rc') == 'y' else '+'}{hit_motif.name}]" | |
| for hit_ele, hit_motif in zip(hit_eles, hit_motifs) | |
| ] | |
| elif record.strand_handling == "unstranded": | |
| motif_strs = [ | |
| f"[{hit_motif.name}]" for hit_ele, hit_motif in zip(hit_eles, hit_motifs) | |
| ] | |
| else: | |
| # TODO - more strand_handling possibilities? | |
| raise Exception(f"Strand handling option {record.strand_handling} not parsable") | |
| tail_length = ( | |
| sequence_length - int(hit_eles[-1].get("pos")) - hit_motifs[-1].length + 1 | |
| ) | |
| motifs_with_gaps = [str(s) for pair in zip(gaps, motif_strs) for s in pair] + [ | |
| str(tail_length) | |
| ] | |
| # remove 0-length gaps | |
| motifs_with_gaps = [s for s in motifs_with_gaps if s != "0"] | |
| return "-".join(motifs_with_gaps) | |
| if __name__ == "__main__": | |
| from Bio._utils import run_doctest | |
| run_doctest() | |