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# Copyright 2015-2015 by Eric Rasche. 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.
"""Bio.Align support for "xmfa" output from Mauve/ProgressiveMauve.
You are expected to use this module via the Bio.Align functions.
"""
from Bio.Align import Alignment
from Bio.Align import interfaces
from Bio.Seq import Seq, reverse_complement
from Bio.SeqRecord import SeqRecord
class AlignmentWriter(interfaces.AlignmentWriter):
"""Mauve xmfa alignment writer."""
fmt = "Mauve"
def __init__(self, target, metadata=None, identifiers=None):
"""Create an AlignmentWriter object.
Arguments:
- target - output stream or file name
- metadata - metadata to be included in the output. If metadata
is None, then the alignments object to be written
must have an attribute `metadata`.
- identifiers - list of the IDs of the sequences included in the
alignment. Sequences will be numbered according to
their index in this list. If identifiers is None,
then the alignments object to be written must have
an attribute `identifiers`.
"""
super().__init__(target)
self._metadata = metadata
self._identifiers = identifiers
def write_header(self, alignments):
"""Write the file header to the output file."""
stream = self.stream
metadata = self._metadata
format_version = metadata.get("FormatVersion", "Mauve1")
line = f"#FormatVersion {format_version}\n"
stream.write(line)
identifiers = self._identifiers
filename = metadata.get("File")
if filename is None:
# sequences came from separate files
for index, filename in enumerate(identifiers):
number = index + 1
line = f"#Sequence{number}File\t{filename}\n"
stream.write(line)
line = f"#Sequence{number}Format\tFastA\n"
stream.write(line)
else:
# sequences came from one combined file
for number, identifier in enumerate(identifiers):
assert number == int(identifier)
number += 1
line = f"#Sequence{number}File\t{filename}\n"
stream.write(line)
line = f"#Sequence{number}Entry\t{number}\n"
stream.write(line)
line = f"#Sequence{number}Format\tFastA\n"
stream.write(line)
backbone_file = metadata.get("BackboneFile")
if backbone_file is not None:
line = f"#BackboneFile\t{backbone_file}\n"
stream.write(line)
def write_file(self, alignments):
"""Write a file with the alignments, and return the number of alignments.
alignments - A Bio.Align.mauve.AlignmentIterator object.
"""
metadata = self._metadata
if metadata is None:
try:
metadata = alignments.metadata
except AttributeError:
raise ValueError("alignments do not have an attribute `metadata`")
else:
self._metadata = metadata
identifiers = self._identifiers
if identifiers is None:
try:
identifiers = alignments.identifiers
except AttributeError:
raise ValueError("alignments do not have an attribute `identifiers`")
else:
self._identifiers = identifiers
count = interfaces.AlignmentWriter.write_file(self, alignments)
return count
def format_alignment(self, alignment):
"""Return a string with a single alignment in the Mauve format."""
metadata = self._metadata
n, m = alignment.shape
if n == 0:
raise ValueError("Must have at least one sequence")
if m == 0:
raise ValueError("Non-empty sequences are required")
filename = metadata.get("File")
lines = []
for i in range(n):
identifier = alignment.sequences[i].id
start = alignment.coordinates[i, 0]
end = alignment.coordinates[i, -1]
if start <= end:
strand = "+"
else:
strand = "-"
start, end = end, start
if start == end:
assert start == 0
else:
start += 1 # switch to 1-based counting
sequence = alignment[i]
if filename is None:
number = (
self._identifiers.index(identifier) + 1
) # Switch to 1-based counting
line = f"> {number}:{start}-{end} {strand} {identifier}\n"
else:
number = int(identifier) + 1 # Switch to 1-based counting
line = f"> {number}:{start}-{end} {strand} {filename}\n"
lines.append(line)
line = f"{sequence}\n"
lines.append(line)
lines.append("=\n")
return "".join(lines)
class AlignmentIterator(interfaces.AlignmentIterator):
"""Mauve xmfa alignment iterator."""
fmt = "Mauve"
def _read_header(self, stream):
metadata = {}
prefix = "Sequence"
suffixes = ("File", "Entry", "Format")
id_info = {}
for suffix in suffixes:
id_info[suffix] = []
for line in stream:
if not line.startswith("#"):
self._line = line.strip()
break
key, value = line[1:].split()
if key.startswith(prefix):
for suffix in suffixes:
if key.endswith(suffix):
break
else:
raise ValueError("Unexpected keyword '%s'" % key)
if suffix == "Entry":
value = int(value) - 1 # Switch to 0-based counting
seq_num = int(key[len(prefix) : -len(suffix)])
id_info[suffix].append(value)
assert seq_num == len(id_info[suffix]) # Mauve uses 1-based counting
else:
metadata[key] = value.strip()
else:
if not metadata:
raise ValueError("Empty file.") from None
if len(set(id_info["File"])) == 1:
# A single file containing all sequences was provided as input;
# store the file name once, and use the entry number as ID
metadata["File"] = id_info["File"][0]
self.identifiers = [str(entry) for entry in id_info["Entry"]]
else:
assert len(set(id_info["File"])) == len(id_info["File"])
# Separate files for each of the sequences were provided as input;
# use the sequence file as ID
self.identifiers = id_info["File"]
self.metadata = metadata
def _parse_description(self, line):
assert line.startswith(">")
locus, strand, comments = line[1:].split(None, 2)
seq_num, start_end = locus.split(":")
seq_num = int(seq_num) - 1 # python counting
identifier = self.identifiers[seq_num]
assert strand in "+-"
start, end = start_end.split("-")
start = int(start)
end = int(end)
if start == 0:
assert end == 0 # unaligned sequence
else:
start -= 1 # python counting
return (identifier, start, end, strand, comments)
def _read_next_alignment(self, stream):
descriptions = []
seqs = []
try:
line = self._line
except AttributeError:
pass
else:
del self._line
description = self._parse_description(line)
identifier, start, end, strand, comments = description
descriptions.append(description)
seqs.append("")
for line in stream:
line = line.strip()
if line.startswith("="):
# There may be more data, but we've reached the end of this
# alignment
coordinates = Alignment.infer_coordinates(seqs)
records = []
for index, (description, seq) in enumerate(zip(descriptions, seqs)):
identifier, start, end, strand, comments = description
seq = seq.replace("-", "")
assert len(seq) == end - start
if strand == "+":
pass
elif strand == "-":
seq = reverse_complement(seq, inplace=False)
coordinates[index, :] = len(seq) - coordinates[index, :]
else:
raise ValueError("Unexpected strand '%s'" % strand)
coordinates[index] += start
if start == 0:
seq = Seq(seq)
else:
seq = Seq({start: seq}, length=end)
record = SeqRecord(seq, id=identifier, description=comments)
records.append(record)
return Alignment(records, coordinates)
elif line.startswith(">"):
description = self._parse_description(line)
identifier, start, end, strand, comments = description
descriptions.append(description)
seqs.append("")
else:
seqs[-1] += line
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