#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2013-2020 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)
[docs]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
[docs] 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 not "label" in qf:
try:
qf["label"] = qf["note"]
except KeyError:
qf["label"] = ["feat{}".format(len(feature))]
if not "ApEinfo_fwdcolor" in qf:
qf["ApEinfo_fwdcolor"] = "#ddfeff"
if not "ApEinfo_revcolor" 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"))
[docs]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