#!/usr/bin/env python

#  Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
#
#  This software is distributed under the MIT Open Source License.
#  <http://www.opensource.org/licenses/mit-license.html>
#
#  Permission is hereby granted, free of charge, to any person obtaining a
#  copy of this software and associated documentation files (the "Software"),
#  to deal in the Software without restriction, including without limitation
#  the rights to use, copy, modify, merge, publish, distribute, sublicense,
#  and/or sell copies of the Software, and to permit persons to whom the
#  Software is furnished to do so, subject to the following conditions:
#
#  The above copyright notice and this permission notice shall be included
#  in all copies or substantial portions of the Software.
#
#  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
#  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
#  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
#  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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"""Read and write sequence information in tab-delimited format.

This very simple format has two columns per line. The first column is a sequence name, the second
column is the sequence itself. The columns are separated by a single tab ("\\t") character.

"""

from typing import Iterator, List, TextIO

from ..seq import Alphabet, Seq, SeqList

names = ("table", "tab")
extensions = ("tbl",)

example = """
EC0001	MKRISTTITTTITITTGNGAG
EC0002	MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAM
EC0003	MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLG
EC0004	MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLD
EC0005	MKKMQSIVLALSLVLVAPMAAQAAEITLVPSVKLQIGDRDNRGYYWDGGH
EC0006	MLILISPAKTLDYQSPLTTTRYTLPELLDNSQQLIHEARKLTPPQISTLM
EC0007	MPDFFSFINSVLWGSVMIYLLFGAGCWFTFRTGFVQFRYIRQFGKSLKNS
EC0008	MTDKLTSLRQYTTVVADTGDIAAMKLYQPQDATTNPSLILNAAQIPEYRK
EC0009	MNTLRIGLVSISDRASSGVYQDKGIPALEEWLTSALTTPFELETRLIPDE
EC0010	MGNTKLANPAPLGLMGFGMTTILLNLHNVGYFALDGIILAMGIFYGGIAQ
"""


def read(fin: TextIO, alphabet: Alphabet = None) -> SeqList:
    """Read and parse file.

    Args:
        fin -- A stream or file to read
        alphabet -- The expected alphabet of the data, if given
    Returns:
        SeqList -- A list of sequences
    Raises:
        ValueError -- If the file is unparsable
    """
    seqs = [s for s in iterseq(fin, alphabet)]
    return SeqList(seqs)


def iterseq(fin: TextIO, alphabet: Alphabet = None) -> Iterator[Seq]:
    """Parse a file and generate sequences.

    Args:
        fin -- A stream or file to read
        alphabet -- The expected alphabet of the data, if given
    Yields:
        Seq -- One alphabetic sequence at a time.
    Raises:
        ValueError -- If the file is unparsable
    """
    alphabet = Alphabet(alphabet)

    for lineno, line in enumerate(fin):
        line = line.strip()
        if line == "":
            continue

        columns = line.split("\t")
        if len(columns) != 2:
            raise ValueError(
                "Parse failed on line %d: did not find two columns separated by a tab."
                % lineno
            )
        yield Seq(columns[1], alphabet=alphabet, name=columns[0])


def write(fout: TextIO, seqs: List[Seq]) -> None:
    """Write a two column, tab-delimited file.

    Args:
        fout -- A writable stream.
        seqs  -- A list of Seq's
    """
    for s in seqs:
        writeseq(fout, s)


def writeseq(fout: TextIO, seq: Seq) -> None:
    """Write a single sequence in fasta format.

    Args:
        afile -- A writable stream.
        seq  -- A Seq instance
    """
    name = seq.name or ""
    print(name, seq, sep="\t", file=fout)