BjornFJohansson/pydna

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2013-2023 by Björn Johansson.  All rights reserved.
# This code is part of the Python-dna distribution and governed by its
# license.  Please see the LICENSE.txt file that should have been included
# as part of this package.
"""This module provides a class for opening a sequence using an editor
that accepts a file as a command line argument.

ApE - A plasmid Editor [#]_ is and excellent editor for this purpose.

References
----------

.. [#] http://biologylabs.utah.edu/jorgensen/wayned/ape/

"""

import time as _time
import tempfile as _tempfile
import os as _os
import subprocess as _subprocess
import operator as _operator
import string as _string
import copy as _copy
import uuid as _uuid

_wl = "{}{}-_.()".format(_string.ascii_letters, _string.digits)


class Editor:
    """
    The Editor class needs to be instantiated before use.

    Parameters
    ----------

    shell_command_for_editor : str
        String containing the path to the editor

    tmpdir : str, optional
        String containing path to the temprary directory where sequence
        files are stored before opening.

    Examples
    --------

    >>> import pydna
    >>> #ape = pydna.Editor("tclsh8.6 /home/bjorn/.ApE/apeextractor/ApE.vfs/lib/app-AppMain/AppMain.tcl")
    >>> #ape.open("aaa") # This command opens the sequence in the ApE editor

    """

    def __init__(self, shell_command_for_editor, tmpdir=None):
        self.path_to_editor = shell_command_for_editor
        self.tmpdir = tmpdir or _os.path.join(_tempfile.gettempdir(), "ApE")
        try:
            _os.makedirs(self.tmpdir)
        except OSError:
            pass

    def open(self, seq_to_open):
        """Open a sequence for editing in an external (DNA) editor.

        Parameters
        ----------
        args : SeqRecord or Dseqrecord object

        """
        seq = _copy.deepcopy(seq_to_open)
        for feature in seq.features:
            qf = feature.qualifiers
            if "label" not in qf:
                try:
                    qf["label"] = qf["note"]
                except KeyError:
                    qf["label"] = ["feat{}".format(len(feature))]
            if "ApEinfo_fwdcolor" not in qf:
                qf["ApEinfo_fwdcolor"] = "#ffff49"
            if "ApEinfo_revcolor" not in qf:
                qf["ApEinfo_revcolor"] = "#ffe6cc"

        seq.features.sort(key=_operator.attrgetter("location.start"))
        name = "{name}.gb".format(
            name="".join(c for c in seq.name.strip().replace(" ", "_") if c in _wl)
            or _uuid.uuid3(_uuid.NAMESPACE_DNS, seq.name)
        )
        tdir = _tempfile.mkdtemp(dir=self.tmpdir)
        tpth = _os.path.join(tdir, name)

        with open(tpth, "w") as f:
            f.write(seq.format("gb"))

        _subprocess.Popen(
            "{} {}".format(self.path_to_editor, tpth),
            shell=True,
            stdout=_tempfile.TemporaryFile(),
            stderr=_tempfile.TemporaryFile(),
        ).pid
        _time.sleep(0.5)


apeloader = Editor(_os.getenv("pydna_ape"))


def ape(*args, **kwargs):
    """docstring."""
    return apeloader.open(*args, **kwargs)


if __name__ == "__main__":
    import os as _os

    cached = _os.getenv("pydna_cached_funcs", "")
    _os.environ["pydna_cached_funcs"] = ""
    import doctest

    doctest.testmod(verbose=True, optionflags=doctest.ELLIPSIS)
    _os.environ["pydna_cached_funcs"] = cached