.venv_haddock/lib/python3.12/site-packages/Bio/Sequencing/Phd.py

# Copyright 2004 by Cymon J. Cox and Frank Kauff.  All rights reserved.
# Copyright 2008 by Michiel de Hoon.  All rights reserved.
# Revisions copyright 2009 by Cymon J. Cox.  All rights reserved.
# Revisions copyright 2009 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.
"""Parser for PHD files output by PHRED and used by PHRAP and CONSED.

This module can be used directly, which will return Record objects
containing all the original data in the file.

Alternatively, using Bio.SeqIO with the "phd" format will call this module
internally.  This will give SeqRecord objects for each contig sequence.
"""

from Bio import Seq

CKEYWORDS = [
    "CHROMAT_FILE",
    "ABI_THUMBPRINT",
    "PHRED_VERSION",
    "CALL_METHOD",
    "QUALITY_LEVELS",
    "TIME",
    "TRACE_ARRAY_MIN_INDEX",
    "TRACE_ARRAY_MAX_INDEX",
    "TRIM",
    "TRACE_PEAK_AREA_RATIO",
    "CHEM",
    "DYE",
]


class Record:
    """Hold information from a PHD file."""

    def __init__(self):
        """Initialize the class."""
        self.file_name = ""
        self.comments = {}
        for kw in CKEYWORDS:
            self.comments[kw.lower()] = None
        self.sites = []
        self.seq = ""
        self.seq_trimmed = ""


def read(source):
    """Read one PHD record from the file and return it as a Record object.

    Argument source is a file-like object opened in text mode, or a path
    to a file.

    This function reads PHD file data line by line from the source, and
    returns a single Record object. A ValueError is raised if more than
    one record is found in the file.
    """
    handle = _open(source)
    try:
        record = _read(handle)
        try:
            next(handle)
        except StopIteration:
            return record
        else:
            raise ValueError("More than one PHD record found")
    finally:
        if handle is not source:
            handle.close()


def parse(source):
    """Iterate over a file yielding multiple PHD records.

    Argument source is a file-like object opened in text mode, or a path
    to a file.

    The data is read line by line from the source.

    Typical usage::

        records = parse(handle)
        for record in records:
            # do something with the record object

    """
    handle = _open(source)
    try:
        while True:
            record = _read(handle)
            if not record:
                return
            yield record
    finally:
        if handle is not source:
            handle.close()


# Everything below is considered private


def _open(source):
    try:
        handle = open(source)
    except TypeError:
        handle = source
        if handle.read(0) != "":
            raise ValueError("PHD files must be opened in text mode.") from None
    return handle


def _read(handle):
    for line in handle:
        if line.startswith("BEGIN_SEQUENCE"):
            record = Record()
            record.file_name = line[15:].rstrip()
            break
    else:
        return  # No record found

    for line in handle:
        if line.startswith("BEGIN_COMMENT"):
            break
    else:
        raise ValueError("Failed to find BEGIN_COMMENT line")

    for line in handle:
        line = line.strip()
        if not line:
            continue
        if line == "END_COMMENT":
            break
        keyword, value = line.split(":", 1)
        keyword = keyword.lower()
        value = value.strip()
        if keyword in (
            "chromat_file",
            "phred_version",
            "call_method",
            "chem",
            "dye",
            "time",
            "basecaller_version",
            "trace_processor_version",
        ):
            record.comments[keyword] = value
        elif keyword in (
            "abi_thumbprint",
            "quality_levels",
            "trace_array_min_index",
            "trace_array_max_index",
        ):
            record.comments[keyword] = int(value)
        elif keyword == "trace_peak_area_ratio":
            record.comments[keyword] = float(value)
        elif keyword == "trim":
            first, last, prob = value.split()
            record.comments[keyword] = (int(first), int(last), float(prob))
    else:
        raise ValueError("Failed to find END_COMMENT line")

    for line in handle:
        if line.startswith("BEGIN_DNA"):
            break
    else:
        raise ValueError("Failed to find BEGIN_DNA line")

    for line in handle:
        if line.startswith("END_DNA"):
            break
        else:
            # Line is: "site quality peak_location"
            # Peak location is optional according to
            # David Gordon (the Consed author)
            parts = line.split()
            if len(parts) in [2, 3]:
                record.sites.append(tuple(parts))
            else:
                raise ValueError(
                    "DNA line must contain a base and quality "
                    "score, and optionally a peak location."
                )

    for line in handle:
        if line.startswith("END_SEQUENCE"):
            break
    else:
        raise ValueError("Failed to find END_SEQUENCE line")

    record.seq = Seq.Seq("".join(n[0] for n in record.sites))
    if record.comments["trim"] is not None:
        first, last = record.comments["trim"][:2]
        record.seq_trimmed = record.seq[first:last]

    return record


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

    run_doctest()