myenv/lib/python3.10/site-packages/Bio/SeqIO/IgIO.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 "ig" (IntelliGenetics or MASE) file format.

This module is for reading and writing IntelliGenetics format files as
SeqRecord objects.  This file format appears to be the same as the MASE
multiple sequence alignment format.

You are expected to use this module via the Bio.SeqIO functions.
"""
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord

from .Interfaces import SequenceIterator


class IgIterator(SequenceIterator):
    """Parser for IntelliGenetics files."""

    def __init__(self, source):
        """Iterate over IntelliGenetics records (as SeqRecord objects).

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

        The optional free format file header lines (which start with two
        semi-colons) are ignored.

        The free format commentary lines at the start of each record (which
        start with a semi-colon) are recorded as a single string with embedded
        new line characters in the SeqRecord's annotations dictionary under the
        key 'comment'.

        Examples
        --------
        >>> with open("IntelliGenetics/TAT_mase_nuc.txt") as handle:
        ...     for record in IgIterator(handle):
        ...         print("%s length %i" % (record.id, len(record)))
        ...
        A_U455 length 303
        B_HXB2R length 306
        C_UG268A length 267
        D_ELI length 309
        F_BZ163A length 309
        O_ANT70 length 342
        O_MVP5180 length 348
        CPZGAB length 309
        CPZANT length 309
        A_ROD length 390
        B_EHOA length 420
        D_MM251 length 390
        STM_STM length 387
        VER_AGM3 length 354
        GRI_AGM677 length 264
        SAB_SAB1C length 219
        SYK_SYK length 330

        """
        super().__init__(source, mode="t", fmt="IntelliGenetics")

    def parse(self, handle):
        """Start parsing the file, and return a SeqRecord generator."""
        records = self.iterate(handle)
        return records

    def iterate(self, handle):
        """Iterate over the records in the IntelliGenetics file."""
        # Skip any file header text before the first record (;; lines)
        for line in handle:
            if not line.startswith(";;"):
                break
        else:
            # Empty file, or header only
            return

        if line[0] != ";":
            raise ValueError(f"Records should start with ';' and not:\n{line!r}")
        while line:
            # Now iterate over the records

            # Try and agree with SeqRecord convention from the GenBank parser,
            # (and followed in the SwissProt parser) which stores the comments
            # as a long string with newlines under annotations key 'comment'.

            # Note some examples use "; ..." and others ";..."
            comment_lines = []
            while line.startswith(";"):
                # TODO - Extract identifier from lines like "LOCUS\tB_SF2"?
                comment_lines.append(line[1:].strip())
                line = next(handle)
            title = line.rstrip()

            seq_lines = []
            for line in handle:
                if line[0] == ";":
                    break
                # Remove trailing whitespace, and any internal spaces
                seq_lines.append(line.rstrip().replace(" ", ""))
            else:
                line = None
            seq_str = "".join(seq_lines)
            if seq_str.endswith("1"):
                # Remove the optional terminator (digit one)
                seq_str = seq_str[:-1]
            if "1" in seq_str:
                raise ValueError(
                    "Potential terminator digit one found within sequence."
                )

            # Return the record and then continue...
            yield SeqRecord(
                Seq(seq_str),
                id=title,
                name=title,
                annotations={"comment": "\n".join(comment_lines)},
            )

        # We should be at the end of the file now
        assert not line


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

    run_doctest(verbose=0)