#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2013-2021 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.
"""
:copyright: Copyright 2013-2021 by Björn Johansson. All rights reserved.
:license: This code is part of the pydna package, governed by the
license in LICENSE.txt that should be included as part
of this package.
pydna
=====
Pydna is a python package providing code for simulation of the creation of
recombinant DNA molecules using
`molecular biology <https://en.wikipedia.org/wiki/Molecular_biology>`_
techniques. Development of pydna happens in this Github `repository <https://github.com/BjornFJohansson/pydna>`_.
Provided:
1. PCR simulation
2. Assembly simulation based on shared identical sequences
3. Primer design for amplification of a given sequence
4. Automatic design of primer tails for Gibson assembly
or homologous recombination.
5. Restriction digestion and cut&paste cloning
6. Agarose gel simulation
7. Download sequences from Genbank
8. Parsing various sequence formats including the capacity to
handle broken Genbank format
pydna package layout
--------------------
The most important modules and how to import functions or classes from
them are listed below. Class names starts with a capital letter,
functions with a lowercase letter:
::
from pydna.module import function
from pydna.module import Class
Example: from pydna.gel import Gel
pydna
├── amplify
│ ├── Anneal
│ └── pcr
├── assembly
│ └── Assembly
├── design
│ ├── assembly_fragments
│ └── primer_design
├── download
│ └── download_text
├── dseqrecord
│ └── Dseqrecord
├── gel
│ └── Gel
├── genbank
│ ├── genbank
│ └── Genbank
├── parsers
│ ├── parse
│ └── parse_primers
└── readers
├── read
└── read_primers
How to use the documentation
----------------------------
Documentation is available as docstrings provided in the source code for
each module.
These docstrings can be inspected by reading the source code directly.
See further below on how to obtain the code for pydna.
In the python shell, use the built-in ``help`` function to view a
function's docstring::
>>> from pydna import readers
>>> help(readers.read)
... # doctest: +SKIP
The doctrings are also used to provide an automaticly generated reference
manual available online at
`read the docs <https://pydna.readthedocs.io>`_.
Docstrings can be explored using `IPython <http://ipython.org/>`_, an
advanced Python shell with
TAB-completion and introspection capabilities. To see which functions
are available in `pydna`,
type `pydna.<TAB>` (where `<TAB>` refers to the TAB key).
Use `pydna.open_config_folder?<ENTER>`to view the docstring or
`pydna.open_config_folder??<ENTER>` to view the source code.
In the `Spyder IDE <https://github.com/spyder-ide/spyder>`_ it is possible
to place the cursor immediately before the name of a module,class or
function and press ctrl+i to bring up docstrings in a separate window in Spyder
Code snippets are indicated by three greater-than signs::
>>> x=41
>>> x=x+1
>>> x
42
pydna source code
-----------------
The pydna source code is
`available on Github <https://github.com/BjornFJohansson/pydna>`_.
How to get more help
--------------------
Please join the
`Google group <https://groups.google.com/forum/#!forum/pydna>`_
for pydna, this is the preferred location for help. If you find bugs
in pydna itself, open an issue at the
`Github repository <https://github.com/BjornFJohansson/pydna/issues>`_.
Examples of pydna in use
------------------------
See this repository for a collection of
`examples <https://github.com/BjornFJohansson/pydna-examples>`_.
"""
from pydna import _version
from pydna.utils import open_folder as _open_folder
from pathlib import Path as _Path
import os as _os
import sys as _sys
import logging as _logging
import logging.handlers as _handlers
import appdirs as _appdirs
import configparser as _configparser
from pydna._pretty import PrettyTable as _PrettyTable
from pydna._version import version as __version__
__author__ = "Björn Johansson"
__copyright__ = "Copyright 2013 - 2021 Björn Johansson"
__credits__ = ["Björn Johansson", "Mark Budde"]
__license__ = "BSD"
__maintainer__ = "Björn Johansson"
__email__ = "bjorn_johansson@bio.uminho.pt"
__status__ = "Development" # "Production" #"Prototype"
# create config directory
_os.environ["pydna_config_dir"] = _os.getenv("pydna_config_dir",
_appdirs.user_config_dir("pydna"))
config_dir = _Path(_os.environ["pydna_config_dir"])
config_dir.mkdir(parents=True, exist_ok=True)
# set path for the pydna.ini file
_ini_path = config_dir/"pydna.ini"
# define user_data_dir
user_data_dir = _Path(_appdirs.user_data_dir("pydna"))
default_ini = {"ape": "put/path/to/ape/here",
"cached_funcs": "pydna.genbank.genbank.nucleotide",
"data_dir": str(user_data_dir),
"email": "someone@example.com",
"enzymes": str(user_data_dir/"enzymes.md"),
"log_dir": _appdirs.user_log_dir("pydna"),
"loglevel": str(_logging.WARNING),
"primers": str(user_data_dir/"primers.md")}
# initiate a config parser instance
_parser = _configparser.ConfigParser()
# if a pydna.ini exists, it is read
if _os.path.exists(_ini_path):
_parser.read(_ini_path)
else: # otherwise it is created with default settings
_parser["main"] = default_ini
with open(_ini_path, "w", encoding="utf-8") as f: # TODO needs encoding?
_parser.write(f)
# pydna related environmental variables are set
# from pydna.ini if they are not set already
_main = _parser["main"]
for key in default_ini:
_os.environ[f"pydna_{key}"] = _os.getenv(f"pydna_{key}",
_main.get(key,
default_ini[key]))
logdir = _Path(_os.environ["pydna_log_dir"])
# create log directory if not present
logdir.mkdir(parents=True, exist_ok=True)
_logmsg = "Log directory {}".format(logdir)
# create logger
_logger = _logging.getLogger("pydna")
_logger.setLevel(int(_os.environ["pydna_loglevel"]))
_hdlr = _handlers.RotatingFileHandler(logdir/"pydna.log",
mode="a",
maxBytes=10 * 1024 * 1024,
backupCount=10,
encoding="utf-8")
_formatter = _logging.Formatter(("%(asctime)s %(levelname)s"
" %(funcName)s %(message)s"))
_hdlr.setFormatter(_formatter)
_logger.addHandler(_hdlr)
_logger.info(_logmsg)
_logger.info("Environmental variable pydna_ape = %s",
_os.environ["pydna_ape"])
_logger.info(
"Environmental variable pydna_cached_funcs = %s",
_os.environ["pydna_cached_funcs"]
)
_logger.info(
"Environmental variable pydna_data_dir = %s",
_os.environ["pydna_data_dir"]
)
_logger.info(
"Environmental variable pydna_email = %s",
_os.environ["pydna_email"]
)
_logger.info(
"Environmental variable pydna_log_dir = %s",
_os.environ["pydna_log_dir"]
)
_logger.info(
"Environmental variable pydna_loglevel = %s",
_os.environ["pydna_loglevel"]
)
_logger.info(
"Environmental variable pydna_primers = %s",
_os.environ["pydna_primers"]
)
# create cache directory if not present
_Path(_os.environ["pydna_data_dir"]).mkdir(parents=True, exist_ok=True)
# find out if optional dependecies for gel module are in place
def _missing_modules_for_gel():
import importlib
from importlib import util
_missing = []
for _optm in ["scipy", "PIL", "numpy", "pyparsing", "requests"]:
_missing.extend([_optm] if not util.find_spec(_optm) else [])
del importlib
del util
return _missing
_missing = _missing_modules_for_gel()
if _missing:
_logger.warning(
"gel simulation will NOT be available."
" Missing modules: %s", ", ".join(_missing)
)
else:
_logger.info("gel simulation is available,"
" optional dependencies were found.")
# _sys.modules.pop("pydna._version", None)
_logger.info("__version__ = %s", __version__)
class _PydnaWarning(Warning):
"""Pydna warning.
Pydna uses this warning (or subclasses of it), to make it easy to
silence all warning messages:
>>> import warnings
>>> from pydna import _PydnaWarning
>>> warnings.simplefilter('ignore', _PydnaWarning)
Consult the warnings module documentation for more details.
"""
pass
class _PydnaDeprecationWarning(_PydnaWarning):
"""pydna deprecation warning.
Pydna uses this warning instead of the built in DeprecationWarning
since those are ignored by default since Python 2.7.
To silence all our deprecation warning messages, use:
>>> import warnings
>>> from pydna import _PydnaDeprecationWarning
>>> warnings.simplefilter('ignore', _PydnaDeprecationWarning)
Code marked as deprecated will be removed in a future version
of Pydna. This can be discussed in the Pydna google group:
https://groups.google.com/forum/#!forum/pydna
"""
pass
[docs]def open_current_folder():
"""Open the current working directory.
Opens in the default file manager. The location for this folder is
given by the :func:`os.getcwd` function
"""
return _open_folder(_os.getcwd())
_logger.info("Current working directory = os.getcwd() = %s", _os.getcwd())
[docs]def open_cache_folder():
"""Open the pydna cache folder.
Opens in the default file manager. The location for this folder is stored
in the *pydna_data_dir* environmental variable.
"""
return _open_folder(_os.environ["pydna_data_dir"])
[docs]def open_config_folder():
"""Open the pydna configuration folder.
Opens in the default file manager. The location for this folder is stored
in the *pydna_config_dir* environmental variable.
The `pydna.ini` file can be edited to make pydna quicker to use.
See the documentation of the :class:configparser.ConfigParser´ class.
Below is the content of a typical `pydna.ini` file on a Linux
system.
::
[main]
loglevel=30
email=myemail@example.org
data_dir=/home/bjorn/.local/share/pydna
log_dir=/home/bjorn/.cache/pydna/log
ape=tclsh /home/bjorn/.ApE/AppMain.tcl
cached_funcs=Genbank_nucleotide
primers=/home/bjorn/Dropbox/wikidata/PRIMERS.txt
enzymes=/home/bjorn/Dropbox/wikidata/RestrictionEnzymes.txt
The email address is set to someone@example.com by default. If you change
this to you own address, the :func:`pydna.genbank.genbank` function can be
used to download sequences from Genbank directly without having to
explicitly add the email address.
Pydna can cache results from the following functions or methods:
- :func:`pydna.genbank.Genbank.nucleotide` Genbank_nucleotide
- :func:`pydna.amplify.Anneal` amplify_Anneal
- :func:`pydna.assembly.Assembly` assembly_Assembly
- :func:`pydna.download.download_text` download.download_text
- :func:`pydna.dseqrecord.Dseqrecord.synced` Dseqrecord_synced
These can be added separated by a comma to the cached_funcs entry
in **pydna.ini** file or the pydna_cached_funcs environment variable.
"""
return _open_folder(_os.environ["pydna_config_dir"])
[docs]def open_log_folder():
"""docstring."""
return _open_folder(_os.environ["pydna_log_dir"])
[docs]def get_env():
"""Print a an ascii table containing all environmental variables.
Pydna related variables have names that starts with `pydna_`
"""
_table = _PrettyTable(["Variable", "Value"])
# _table.set_style(_prettytable.DEFAULT)
_table.align["Variable"] = "l" # Left align
_table.align["Value"] = "l" # Left align
_table.padding_width = 1 # One space between column edges and contents
for k, v in sorted(_os.environ.items()):
if k.startswith("pydna"):
_table.add_row([k, v])
return _table
[docs]def logo():
r"""Ascii-art logotype of pydna.
>>> import pydna
>>> print(pydna.logo())
_
| |
____ _ _ __| |___ _____
| _ \| | | |/ _ | _ \(____ |
| |_| | |_| ( (_| | | | / ___ |
| __/ \__ |\____|_| |_\_____|
|_| (____/
<BLANKLINE>
"""
from pydna._pretty import pretty_str as _pretty_str
import textwrap
return _pretty_str(
textwrap.dedent(
r"""
_
| |
____ _ _ __| |___ _____
| _ \| | | |/ _ | _ \(____ |
| |_| | |_| ( (_| | | | / ___ |
| __/ \__ |\____|_| |_\_____|
|_| (____/
"""[
1:
]
)
)
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