#!/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"),
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"""Read and write sequence information in IntelliGenetics format.

A sequence file in IG format can contain several sequences, each consisting of a
number of comment lines that must begin with a semicolon (";"), a line with the
sequence name and the sequence itself terminated with the termination character
'1' for linear or '2' for circular sequences. The termination character is
defacto optional.

--- Example IG File ---

;H.sapiens fau mRNA, 518 bases
HSFAU
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc
actcttaagtcttttgtaattctggctttctctaataaaaaagccactta
gttcagtcaaaaaaaaaa1
;H.sapiens fau 1 gene, 2016 bases
HSFAU1
ctaccattttccctctcgattctatatgtacactcgggacaagttctcct
gatcgaaaacggcaaaactaaggccccaagtaggaatgccttagttttcg
gggttaacaatgattaacactgagcctcacacccacgcgatgccctcagc
tcctcgctcagcgctctcaccaacagccgtagcccgcagccccgctggac
accggttctccatccccgcagcgtagcccggaacatggtagctgccatct
ttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgcccc2

"""

from typing import Iterator, List, Optional, TextIO

from ..seq import Alphabet, Seq, SeqList
from ..utils import remove_whitespace

names = (
    "intelligenetics",
    "ig",
    "stanford",
)
extensions = ("ig",)

example = """
;H.sapiens fau mRNA, 518 bases
HSFAU
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc
actcttaagtcttttgtaattctggctttctctaataaaaaagccactta
gttcagtcaaaaaaaaaa1
;H.sapiens fau 1 gene, 2016 bases
HSFAU1
ctaccattttccctctcgattctatatgtacactcgggacaagttctcct
gatcgaaaacggcaaaactaaggccccaagtaggaatgccttagttttcg
gggttaacaatgattaacactgagcctcacacccacgcgatgccctcagc
tcctcgctcagcgctctcaccaacagccgtagcccgcagccccgctggac
accggttctccatccccgcagcgtagcccggaacatggtagctgccatct
ttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgcccc2
"""


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

    seqs: list = []
    header: list = []
    start_lineno = -1
    name = None

    def build_seq(
        seqs: List[str],
        alphabet: Alphabet,
        name: Optional[str],
        comments: List[str],
        lineno: int,
    ) -> Seq:

        try:
            desc = "\n".join(comments)
            s = Seq("".join(seqs), alphabet, name=name, description=desc)
        except ValueError:
            raise ValueError(
                "Parse failed with sequence starting at line %d: "
                "Character not in alphabet: %s" % (lineno, alphabet)
            )
        return s

    for lineno, line in enumerate(fin):
        line = line.strip()
        if line == "":
            continue
        if line.startswith(";"):
            if seqs:
                # end of sequence
                yield build_seq(seqs, alphabet, name, header, start_lineno)
                header = []
                seqs = []
                name = None
            header.append(line[1:])
            start_lineno = lineno
        elif not name:
            name = line
        elif line[-1] == "1" or line[-1] == "2":
            # End of sequence
            seqs.append(remove_whitespace(line[0:-1]))
            yield build_seq(seqs, alphabet, name, header, start_lineno)
            header = []
            seqs = []
            name = None
        else:
            seqs.append(remove_whitespace(line))

    if seqs:
        yield build_seq(seqs, alphabet, name, header, start_lineno)
    return


def write(fout: TextIO, seqs: SeqList) -> None:
    """Write an IG file.

    Args:
        fout -- A writable stream.
        seqs  -- A list of Seq's
    Raises:
        ValueError -- If a sequence is missing a name
    """
    for s in seqs:
        writeseq(fout, s)


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

    Args:
        fout -- A writable stream.
        seq  -- A Seq instance
    Raises:
        ValueError -- If a sequence is missing a name
    """
    desc = seq.description or ""

    # We prepend ';' to each line
    for h in desc.splitlines():
        print(";" + h, file=fout)
    if not seq.name:
        raise ValueError("Write failed with missing sequence name: %s" % str(seq))
    print(seq.name, file=fout)
    L = len(seq)
    line_length = 80
    for n in range(1 + L // line_length):
        print(seq[n * line_length : (n + 1) * line_length], file=fout)
    print(file=fout)
