.venv_haddock/lib/python3.12/site-packages/Bio/SeqIO/AceIO.py

# Copyright 2008-2015 by Peter Cock.  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.SeqIO support for the "ace" file format.

You are expected to use this module via the Bio.SeqIO functions.
See also the Bio.Sequencing.Ace module which offers more than just accessing
the contig consensus sequences in an ACE file as SeqRecord objects.
"""

from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Sequencing import Ace

from .Interfaces import _TextIOSource
from .Interfaces import SequenceIterator


class AceIterator(SequenceIterator):
    """Return SeqRecord objects from an ACE file."""

    modes = "t"

    def __init__(
        self,
        source: _TextIOSource,
    ) -> None:
        """Iterate over SeqRecord objects read from an ACE file.

        Arguments:
         - source - input stream opened in text mode, or a path to a file

        This uses the Bio.Sequencing.Ace module to do the hard work.  Note that
        by iterating over the file in a single pass, we are forced to ignore any
        WA, CT, RT or WR footer tags.

        Ace files include the base quality for each position, which are taken to
        be PHRED style scores. Just as if you had read in a FASTQ or QUAL file
        using PHRED scores using Bio.SeqIO, these are stored in the SeqRecord's
        letter_annotations dictionary under the "phred_quality" key.

        >>> from Bio import SeqIO
        >>> with open("Ace/consed_sample.ace") as handle:
        ...     for record in SeqIO.parse(handle, "ace"):
        ...         print("%s %s... %i" % (record.id, record.seq[:10], len(record)))
        ...         print(max(record.letter_annotations["phred_quality"]))
        Contig1 agccccgggc... 1475
        90

        However, ACE files do not include a base quality for any gaps in the
        consensus sequence, and these are represented in Biopython with quality
        of zero. Using zero is perhaps misleading as there may be very strong
        evidence to support the gap in the consensus. Previous versions of
        Biopython therefore used None instead, but this complicated usage,
        and prevented output of the gapped sequence as FASTQ format.

        >>> from Bio import SeqIO
        >>> with open("Ace/contig1.ace") as handle:
        ...     for record in SeqIO.parse(handle, "ace"):
        ...         print("%s ...%s..." % (record.id, record.seq[85:95]))
        ...         print(record.letter_annotations["phred_quality"][85:95])
        ...         print(max(record.letter_annotations["phred_quality"]))
        Contig1 ...AGAGG-ATGC...
        [57, 57, 54, 57, 57, 0, 57, 72, 72, 72]
        90
        Contig2 ...GAATTACTAT...
        [68, 68, 68, 68, 68, 68, 68, 68, 68, 68]
        90

        """
        super().__init__(source, fmt="ACE")
        self.ace_contigs = Ace.parse(self.stream)

    def __next__(self):
        try:
            ace_contig = next(self.ace_contigs)
        except StopIteration:
            raise StopIteration from None
        # Convert the ACE contig record into a SeqRecord...
        consensus_seq_str = ace_contig.sequence
        if "*" in consensus_seq_str:
            # For consistency with most other file formats, map
            # any * gaps into - gaps.
            assert "-" not in consensus_seq_str
            consensus_seq = Seq(consensus_seq_str.replace("*", "-"))
        else:
            consensus_seq = Seq(consensus_seq_str)

        # TODO? - Base segments (BS lines) which indicates which read
        # phrap has chosen to be the consensus at a particular position.
        # Perhaps as SeqFeature objects?

        # TODO - Supporting reads (RD lines, plus perhaps QA and DS lines)
        # Perhaps as SeqFeature objects?

        seq_record = SeqRecord(consensus_seq, id=ace_contig.name, name=ace_contig.name)

        # Consensus base quality (BQ lines).  Note that any gaps (originally
        # as * characters) in the consensus do not get a quality entry, so
        # we assign a quality of None (zero would be misleading as there may
        # be excellent support for having a gap here).
        quals = []
        i = 0
        for base in consensus_seq:
            if base == "-":
                quals.append(0)
            else:
                quals.append(ace_contig.quality[i])
                i += 1
        assert i == len(ace_contig.quality)
        seq_record.letter_annotations["phred_quality"] = quals

        return seq_record


if __name__ == "__main__":
    from Bio._utils import run_doctest

    run_doctest()