.venv_haddock/lib/python3.12/site-packages/Bio/AlignIO/MauveIO.py

# 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.AlignIO support for "xmfa" output from Mauve/ProgressiveMauve.

You are expected to use this module via the Bio.AlignIO functions (or the
Bio.SeqIO functions if you want to work directly with the gapped sequences).

For example, consider a progressiveMauve alignment file containing the following::

    #FormatVersion Mauve1
    #Sequence1File	a.fa
    #Sequence1Entry	1
    #Sequence1Format	FastA
    #Sequence2File	b.fa
    #Sequence2Entry	2
    #Sequence2Format	FastA
    #Sequence3File	c.fa
    #Sequence3Entry	3
    #Sequence3Format	FastA
    #BackboneFile	three.xmfa.bbcols
    > 1:0-0 + a.fa
    --------------------------------------------------------------------------------
    --------------------------------------------------------------------------------
    --------------------------------------------------------------------------------
    > 2:5417-5968 + b.fa
    TTTAAACATCCCTCGGCCCGTCGCCCTTTTATAATAGCAGTACGTGAGAGGAGCGCCCTAAGCTTTGGGAAATTCAAGC-
    --------------------------------------------------------------------------------
    CTGGAACGTACTTGCTGGTTTCGCTACTATTTCAAACAAGTTAGAGGCCGTTACCTCGGGCGAACGTATAAACCATTCTG
    > 3:9476-10076 - c.fa
    TTTAAACACCTTTTTGGATG--GCCCAGTTCGTTCAGTTGTG-GGGAGGAGATCGCCCCAAACGTATGGTGAGTCGGGCG
    TTTCCTATAGCTATAGGACCAATCCACTTACCATACGCCCGGCGTCGCCCAGTCCGGTTCGGTACCCTCCATGACCCACG
    ---------------------------------------------------------AAATGAGGGCCCAGGGTATGCTT
    =
    > 2:5969-6015 + b.fa
    -----------------------
    GGGCGAACGTATAAACCATTCTG
    > 3:9429-9476 - c.fa
    TTCGGTACCCTCCATGACCCACG
    AAATGAGGGCCCAGGGTATGCTT

This is a multiple sequence alignment with multiple aligned sections, so you
would probably load this using the Bio.AlignIO.parse() function:

    >>> from Bio import AlignIO
    >>> align = AlignIO.parse("Mauve/simple_short.xmfa", "mauve")
    >>> alignments = list(align)
    >>> for aln in alignments:
    ...     print(aln)
    ...
    Alignment with 3 rows and 240 columns
    --------------------------------------------...--- a.fa
    TTTAAACATCCCTCGGCCCGTCGCCCTTTTATAATAGCAGTACG...CTG b.fa/5416-5968
    TTTAAACACCTTTTTGGATG--GCCCAGTTCGTTCAGTTGTG-G...CTT c.fa/9475-10076
    Alignment with 2 rows and 46 columns
    -----------------------GGGCGAACGTATAAACCATTCTG b.fa/5968-6015
    TTCGGTACCCTCCATGACCCACGAAATGAGGGCCCAGGGTATGCTT c.fa/9428-9476

Additional information is extracted from the XMFA file and available through
the annotation attribute of each record::

    >>> for record in alignments[0]:
    ...     print(record.id, len(record))
    ...     print("  start: %d, end: %d, strand: %d" %(
    ...         record.annotations['start'], record.annotations['end'],
    ...         record.annotations['strand']))
    ...
    a.fa 240
      start: 0, end: 0, strand: 1
    b.fa/5416-5968 240
      start: 5416, end: 5968, strand: 1
    c.fa/9475-10076 240
      start: 9475, end: 10076, strand: -1

"""

import re

from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord

from .Interfaces import AlignmentIterator
from .Interfaces import SequentialAlignmentWriter

XMFA_HEADER_REGEX = re.compile(
    r"> (?P<id>\d+):(?P<start>\d+)-(?P<end>\d+) (?P<strand>[+-]) (?P<name>.*)"
)
XMFA_HEADER_REGEX_BIOPYTHON = re.compile(
    r"> (?P<id>\d+):(?P<start>\d+)-(?P<end>\d+) (?P<strand>[+-]) (?P<name>[^#]*) # (?P<realname>.*)"
)
ID_LINE_FMT = "> {seq_name}:{start}-{end} {strand} {filename} # {ugly_hack}"


def _identifier_split(identifier):
    """Return (name, start, end) string tuple from an identifier (PRIVATE)."""
    id, loc, strand = identifier.split(":")
    start, end = map(int, loc.split("-"))
    start -= 1
    return id, start, end, strand


class MauveWriter(SequentialAlignmentWriter):
    """Mauve/XMFA alignment writer."""

    def __init__(self, *args, **kwargs):
        """Initialize the class."""
        super().__init__(*args, **kwargs)
        self._wrote_header = False
        self._wrote_first = False

    def write_alignment(self, alignment):
        """Use this to write (another) single alignment to an open file.

        Note that sequences and their annotation are recorded
        together (rather than having a block of annotation followed
        by a block of aligned sequences).
        """
        count = len(alignment)

        self._length_of_sequences = alignment.get_alignment_length()

        # NOTE - For now, the alignment object does not hold any per column
        # or per alignment annotation - only per sequence.

        if count == 0:
            raise ValueError("Must have at least one sequence")
        if self._length_of_sequences == 0:
            raise ValueError("Non-empty sequences are required")

        if not self._wrote_header:
            self._wrote_header = True
            self.handle.write("#FormatVersion Mauve1\n")
            # There are some more headers, but we ignore those for now.
            # Sequence1File	unknown.fa
            # Sequence1Entry	1
            # Sequence1Format	FastA
            for i in range(1, count + 1):
                self.handle.write(f"#Sequence{i}Entry\t{i}\n")

        for idx, record in enumerate(alignment):
            self._write_record(record, record_idx=idx)
        self.handle.write("=\n")

    def _write_record(self, record, record_idx=0):
        """Write a single SeqRecord to the file (PRIVATE)."""
        if self._length_of_sequences != len(record.seq):
            raise ValueError("Sequences must all be the same length")

        seq_name = record.name
        try:
            seq_name = str(int(record.name))
        except ValueError:
            seq_name = str(record_idx + 1)

        # We remove the "/{start}-{end}" before writing, as it cannot be part
        # of the produced XMFA file.
        if "start" in record.annotations and "end" in record.annotations:
            suffix0 = f"/{record.annotations['start']}-{record.annotations['end']}"
            suffix1 = f"/{record.annotations['start'] + 1}-{record.annotations['end']}"
            if seq_name[-len(suffix0) :] == suffix0:
                seq_name = seq_name[: -len(suffix0)]
            if seq_name[-len(suffix1) :] == suffix1:
                seq_name = seq_name[: -len(suffix1)]

        if (
            "start" in record.annotations
            and "end" in record.annotations
            and "strand" in record.annotations
        ):
            id_line = ID_LINE_FMT.format(
                seq_name=seq_name,
                start=record.annotations["start"] + 1,
                end=record.annotations["end"],
                strand=("+" if record.annotations["strand"] == 1 else "-"),
                filename=record.name + ".fa",
                ugly_hack=record.id,
            )
            lacking_annotations = False
        else:
            id_line = ID_LINE_FMT.format(
                seq_name=seq_name,
                start=0,
                end=0,
                strand="+",
                filename=record.name + ".fa",
                ugly_hack=record.id,
            )
            lacking_annotations = True

        # If the sequence is an empty one, skip writing it out
        if (":0-0 " in id_line or ":1-0 " in id_line) and not lacking_annotations:
            # Except in the first LCB
            if not self._wrote_first:
                self._wrote_first = True
                # The first LCB we write out is special, and must list ALL
                # sequences, for the Mauve GUI
                # http://darlinglab.org/mauve/user-guide/files.html#non-standard-xmfa-formatting-used-by-the-mauve-gui
                id_line = ID_LINE_FMT.format(
                    seq_name=seq_name,
                    start=0,
                    end=0,
                    strand="+",
                    filename=record.name + ".fa",
                    ugly_hack=record.id,
                )
                id_line = id_line.replace("\n", " ").replace("\r", " ")
                self.handle.write(id_line + "\n\n")
            # Alignments lacking a start/stop/strand were generated by
            # Biopython on load, and shouldn't exist according to XMFA
        else:
            # In other blocks, we only write sequences if they exist in a given
            # alignment.
            id_line = id_line.replace("\n", " ").replace("\r", " ")
            self.handle.write(id_line + "\n")
            for i in range(0, len(record.seq), 80):
                self.handle.write(f"{record.seq[i : i + 80]}\n")


class MauveIterator(AlignmentIterator):
    """Mauve xmfa alignment iterator."""

    _ids: list[str] = []  # for caching IDs between __next__ calls

    def __next__(self):
        """Parse the next alignment from the handle."""
        handle = self.handle
        line = handle.readline()

        if not line:
            raise StopIteration

        # Strip out header comments
        while line and line.strip().startswith("#"):
            line = handle.readline()

        seqs = {}
        seq_regions = {}
        passed_end_alignment = False

        latest_id = None
        while True:
            if not line:
                break  # end of file
            line = line.strip()

            if line.startswith("="):
                # There may be more data, but we've reached the end of this
                # alignment
                break
            elif line.startswith(">"):
                m = XMFA_HEADER_REGEX_BIOPYTHON.match(line)
                if not m:
                    m = XMFA_HEADER_REGEX.match(line)
                    if not m:
                        raise ValueError("Malformed header line: %s", line)

                parsed_id = m.group("id")
                parsed_data = {}
                for key in ("start", "end", "id", "strand", "name", "realname"):
                    try:
                        value = m.group(key)
                        if key == "start":
                            value = int(value)
                            # Convert to zero based counting
                            if value > 0:
                                value -= 1

                        if key == "end":
                            value = int(value)
                        parsed_data[key] = value
                    except IndexError:
                        # This will occur if we're asking for a group that
                        # doesn't exist. It's fine.
                        pass
                seq_regions[parsed_id] = parsed_data

                if parsed_id not in self._ids:
                    self._ids.append(parsed_id)

                seqs.setdefault(parsed_id, "")
                latest_id = parsed_id
            else:
                assert not passed_end_alignment
                if latest_id is None:
                    raise ValueError("Saw sequence before definition line")
                seqs[latest_id] += line
            line = handle.readline()

        assert len(seqs) <= len(self._ids)

        self.ids = self._ids
        self.sequences = seqs

        if self._ids and seqs:
            alignment_length = max(map(len, list(seqs.values())))
            records = []
            for id in self._ids:
                if id not in seqs or len(seqs[id]) == 0 or len(seqs[id]) == 0:
                    seq = "-" * alignment_length
                else:
                    seq = seqs[id]

                if alignment_length != len(seq):
                    raise ValueError(
                        "Sequences have different lengths, or repeated identifier"
                    )

                # Sometimes we don't see a particular sequence in the
                # alignment, so we skip that record since it isn't present in
                # that LCB/alignment
                if id not in seq_regions:
                    continue

                if seq_regions[id]["start"] != 0 or seq_regions[id]["end"] != 0:
                    suffix = "/{start}-{end}".format(**seq_regions[id])
                    if "realname" in seq_regions[id]:
                        corrected_id = seq_regions[id]["realname"]
                    else:
                        corrected_id = seq_regions[id]["name"]
                    if corrected_id.count(suffix) == 0:
                        corrected_id += suffix
                else:
                    if "realname" in seq_regions[id]:
                        corrected_id = seq_regions[id]["realname"]
                    else:
                        corrected_id = seq_regions[id]["name"]

                record = SeqRecord(Seq(seq), id=corrected_id, name=id)

                record.annotations["start"] = seq_regions[id]["start"]
                record.annotations["end"] = seq_regions[id]["end"]
                record.annotations["strand"] = (
                    1 if seq_regions[id]["strand"] == "+" else -1
                )

                records.append(record)
            return MultipleSeqAlignment(records)
        else:
            raise StopIteration