pydna 5.5.1__tar.gz → 5.5.3__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {pydna-5.5.1 → pydna-5.5.3}/PKG-INFO +22 -18
- {pydna-5.5.1 → pydna-5.5.3}/README.md +20 -17
- {pydna-5.5.1 → pydna-5.5.3}/pyproject.toml +11 -7
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/__init__.py +116 -134
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/_pretty.py +2 -14
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/all.py +10 -20
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/amplicon.py +25 -20
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/amplify.py +46 -26
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/assembly.py +50 -27
- pydna-5.5.3/src/pydna/assembly2.py +2627 -0
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/common_sub_strings.py +2 -12
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/contig.py +39 -22
- pydna-5.5.3/src/pydna/cre_lox.py +130 -0
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/crispr.py +8 -13
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/design.py +89 -59
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/download.py +10 -18
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/dseq.py +119 -59
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/dseqrecord.py +88 -45
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/fakeseq.py +0 -11
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/fusionpcr.py +3 -1
- pydna-5.5.3/src/pydna/gateway.py +164 -0
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/gel.py +8 -13
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/genbank.py +33 -32
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/genbankfile.py +8 -13
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/genbankfixer.py +41 -28
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/genbankrecord.py +11 -14
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/goldengate.py +2 -2
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/ladders.py +4 -11
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/ligate.py +8 -14
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/parsers.py +25 -9
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/primer.py +3 -12
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/readers.py +0 -11
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/seq.py +21 -18
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/seqrecord.py +20 -20
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/sequence_picker.py +3 -12
- pydna-5.5.3/src/pydna/sequence_regex.py +44 -0
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/tm.py +13 -15
- pydna-5.5.3/src/pydna/types.py +41 -0
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/utils.py +173 -58
- pydna-5.5.1/src/pydna/editor.py +0 -119
- pydna-5.5.1/src/pydna/gateway.py +0 -162
- pydna-5.5.1/src/pydna/myenzymes.py +0 -51
- pydna-5.5.1/src/pydna/myprimers.py +0 -219
- {pydna-5.5.1 → pydna-5.5.3}/LICENSE.txt +0 -0
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/_thermodynamic_data.py +0 -0
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/codon.py +0 -0
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/conftest.py +0 -0
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/threading_timer_decorator_exit.py +0 -0
- {pydna-5.5.1 → pydna-5.5.3}/src/pydna/user_cloning.py +0 -0
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Metadata-Version: 2.3
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Name: pydna
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Version: 5.5.
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Version: 5.5.3
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Summary: Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules.
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License: BSD
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Author: Björn F. Johansson
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Requires-Dist: pyparsing (>=2.4.7) ; extra == "download"
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Requires-Dist: requests (>=2.26.0) ; extra == "download"
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Requires-Dist: scipy (>=1.11.3) ; (python_version >= "3.12") and (extra == "gel")
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Requires-Dist: scipy (>=1.9.3) ; (python_version < "3.12") and (extra == "gel")
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Project-URL: Repository, https://github.com/pydna-group/pydna/tree/master
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Description-Content-Type: text/markdown
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# 
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| [](https://github.com/pydna-group/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml) | [](https://codecov.io/gh/pydna-group/pydna/branch/master) | [](https://badge.fury.io/py/pydna) | [](https://groups.google.com/g/pydna) |
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| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------- |
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| [](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml) | [](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml) | [](https://github.com/pydna-group/pydna/issues) | [](https://github.com/pydna-group/pydna/stargazers) | |
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<!-- docs/index.rst-start -->
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If you don't have a github account, you can get in touch through the [google group](https://groups.google.com/d/forum/pydna) for pydna.
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Below are the instructions for developers who want to contribute to pydna. Please direct pull requests towards the `
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Below are the instructions for developers who want to contribute to pydna. Please direct pull requests towards the `master` branch.
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### Fork the repository and set up a dev branch 🍴
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Fork the repository. Create your branch starting from `master`, and if your changes are related to an issue, call the branch `issue_<number>`.
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```bash
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# Clone the repository
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```
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> **TIP:** The hooks are a series of checks that will be run before you commit your code. If any of the checks fail, the commit will not be allowed. Some of them auto-fix the code (e.g., `black` formatting), so you can simply do `git add .` and commit again. Others like `flake8` will prevent the commit to happen until the code is compliant. For instance, if you import a module in a file and not use it, `flake8` will complain. For a full list of checks, see `.pre-commit-config.yaml`.
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> **TIP:** The continuous integration pipeline also runs doctests. These are tests that validate that the docstring examples are correct. For example, the docstring of the function `pydna.utils.smallest_rotation` looks like this:
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> ```python
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> 'aaat'
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> ```
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> doctest will fail if `smallest_rotation("taaa")` does not return `'aaat'`. If you make changes to some function, you may break the doctests, and this can be a bit hard to understand. If this happens, the CI tests will fail, with a message similar to this:
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> ```
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> =================================== FAILURES ===================================
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> ___________________ [doctest] pydna.assembly2.blunt_overlap ____________________
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> ```
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> This means that the doctest of the function `blunt_overlap` failed. You can run the same test locally with `python -m doctest src/pydna/assembly2.py` (use the appropriate path to the module file). That will give you information of what's failing. Fix, and re-run until it passes!
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### Creating a PR 🔗
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* From your fork, make a PR towards the branch `master` in the original repository.
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* Mention the issue number in the PR description (e.g., `Closes #123`).
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In Cold Spring Harbor Laboratory (p. 2021.01.17.427048). [DOI](https://doi.org/10.1101/2021.01.17.427048)
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[PubMed](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8180056)
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[An Automated Protein Synthesis Pipeline with Transcriptic and Snakemake](http://blog.booleanbiotech.com/transcriptic_protein_synthesis_pipeline.html)
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| [](https://github.com/pydna-group/pydna/actions/workflows/pydna_test_and_coverage_workflow.yml) | [](https://codecov.io/gh/pydna-group/pydna/branch/master) | [](https://badge.fury.io/py/pydna) | [](https://groups.google.com/g/pydna) |
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| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------- |
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| [](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml) | [](https://github.com/pydna-group/pydna/actions/workflows/publish-docs.yml) | [](https://github.com/pydna-group/pydna/issues) | [](https://github.com/pydna-group/pydna/stargazers) | |
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If you don't have a github account, you can get in touch through the [google group](https://groups.google.com/d/forum/pydna) for pydna.
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Below are the instructions for developers who want to contribute to pydna. Please direct pull requests towards the `
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Below are the instructions for developers who want to contribute to pydna. Please direct pull requests towards the `master` branch.
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```bash
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```
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> **TIP:** The hooks are a series of checks that will be run before you commit your code. If any of the checks fail, the commit will not be allowed. Some of them auto-fix the code (e.g., `black` formatting), so you can simply do `git add .` and commit again. Others like `flake8` will prevent the commit to happen until the code is compliant. For instance, if you import a module in a file and not use it, `flake8` will complain. For a full list of checks, see `.pre-commit-config.yaml`.
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> ```
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> doctest will fail if `smallest_rotation("taaa")` does not return `'aaat'`. If you make changes to some function, you may break the doctests, and this can be a bit hard to understand. If this happens, the CI tests will fail, with a message similar to this:
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> ```
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> ```
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> This means that the doctest of the function `blunt_overlap` failed. You can run the same test locally with `python -m doctest src/pydna/assembly2.py` (use the appropriate path to the module file). That will give you information of what's failing. Fix, and re-run until it passes!
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# create logger
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_hdlr = _handlers.RotatingFileHandler(
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_formatter = _logging.Formatter(("%(asctime)s %(levelname)s" " %(funcName)s %(message)s"))
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_hdlr.setFormatter(_formatter)
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_logger.info(_logmsg)
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_logger.info("Environmental variable pydna_ape = %s", _os.environ["pydna_ape"])
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_logger.info("Environmental variable pydna_cached_funcs = %s", _os.environ["pydna_cached_funcs"])
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_logger.info("Environmental variable pydna_data_dir = %s", _os.environ["pydna_data_dir"])
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_logger.info("Environmental variable pydna_email = %s", _os.environ["pydna_email"])
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_logger.info("Environmental variable pydna_log_dir = %s", _os.environ["pydna_log_dir"])
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_logger.info("Environmental variable pydna_loglevel = %s", _os.environ["pydna_loglevel"])
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_logger.info("Environmental variable pydna_primers = %s", _os.environ["pydna_primers"])
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# _logger = _logging.getLogger("pydna")
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# _logger.setLevel(int(_os.environ["pydna_loglevel"]))
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# _hdlr = _handlers.RotatingFileHandler(
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# logdir / "pydna.log",
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# mode="a",
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# maxBytes=10 * 1024 * 1024,
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# backupCount=10,
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# )
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# _formatter = _logging.Formatter(("%(asctime)s %(levelname)s" " %(funcName)s %(message)s"))
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# _hdlr.setFormatter(_formatter)
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# _logger.addHandler(_hdlr)
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# _logger.info(_logmsg)
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# _logger.info("Environmental variable pydna_ape = %s", _os.environ["pydna_ape"])
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# _logger.info("Environmental variable pydna_cached_funcs = %s", _os.environ["pydna_cached_funcs"])
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# _logger.info("Environmental variable pydna_data_dir = %s", _os.environ["pydna_data_dir"])
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# _logger.info("Environmental variable pydna_email = %s", _os.environ["pydna_email"])
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# _logger.info("Environmental variable pydna_log_dir = %s", _os.environ["pydna_log_dir"])
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# _logger.info("Environmental variable pydna_loglevel = %s", _os.environ["pydna_loglevel"])
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# _logger.info("Environmental variable pydna_primers = %s", _os.environ["pydna_primers"])
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# _logger.info(
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# "Environmental variable pydna_assembly_limit = %s",
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# _os.environ["pydna_assembly_limit"],
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# )
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# create cache directory if not present
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_Path(_os.environ["pydna_data_dir"]).mkdir(parents=True, exist_ok=True)
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# _Path(_os.environ["pydna_data_dir"]).mkdir(parents=True, exist_ok=True)
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# find out if optional dependecies for gel module are in place
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#
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@@ -264,7 +257,7 @@ _Path(_os.environ["pydna_data_dir"]).mkdir(parents=True, exist_ok=True)
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# _logger.info("gel simulation is available," " optional dependencies were found.")
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#
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_logger.info("__version__ = %s", __version__)
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# _logger.info("__version__ = %s", __version__)
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class _PydnaWarning(Warning):
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@@ -304,74 +297,74 @@ class _PydnaDeprecationWarning(_PydnaWarning):
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pass
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def open_current_folder():
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# def open_current_folder():
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# """Open the current working directory.
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# Opens in the default file manager. The location for this folder is
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# given by the :func:`os.getcwd` function
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# """
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# return _open_folder(_os.getcwd())
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_logger.info("Current working directory = os.getcwd() = %s", _os.getcwd())
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# _logger.info("Current working directory = os.getcwd() = %s", _os.getcwd())
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def open_cache_folder():
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# def open_cache_folder():
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# """Open the pydna cache folder.
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# Opens in the default file manager. The location for this folder is stored
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# in the *pydna_data_dir* environmental variable.
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# """
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# return _open_folder(_os.environ["pydna_data_dir"])
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def open_config_folder():
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# def open_config_folder():
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# """Open the pydna configuration folder.
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# Opens in the default file manager. The location for this folder is stored
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# in the *pydna_config_dir* environmental variable.
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# The `pydna.ini` file can be edited to make pydna quicker to use.
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# See the documentation of the :class:configparser.ConfigParser´ class.
|
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# Below is the content of a typical `pydna.ini` file on a Linux
|
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# system.
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# ::
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# [main]
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336
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# loglevel=30
|
|
337
|
+
# email=myemail@example.org
|
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|
+
# data_dir=/home/user/.local/share/pydna
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+
# log_dir=/home/user/.cache/pydna/log
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|
+
# ape=tclsh /path/to/ape/AppMain.tcl
|
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341
|
+
# cached_funcs=Genbank_nucleotide
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|
+
# primers=/path/to/primers/PRIMERS.txt
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+
# enzymes=/path/to/enzymes/RestrictionEnzymes.txt
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354
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355
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345
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# The email address is set to someone@example.com by default. If you change
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|
+
# this to you own address, the :func:`pydna.genbank.genbank` function can be
|
|
347
|
+
# used to download sequences from Genbank directly without having to
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348
|
+
# explicitly add the email address.
|
|
356
349
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357
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-
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350
|
+
# Pydna can cache results from the following functions or methods:
|
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358
351
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|
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359
|
-
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360
|
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361
|
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362
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363
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352
|
+
# - :func:`pydna.genbank.Genbank.nucleotide` Genbank_nucleotide
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|
353
|
+
# - :func:`pydna.amplify.Anneal` amplify_Anneal
|
|
354
|
+
# - :func:`pydna.assembly.Assembly` assembly_Assembly
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|
355
|
+
# - :func:`pydna.download.download_text` download.download_text
|
|
356
|
+
# - :func:`pydna.dseqrecord.Dseqrecord.synced` Dseqrecord_synced
|
|
364
357
|
|
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365
|
-
|
|
366
|
-
|
|
358
|
+
# These can be added separated by a comma to the cached_funcs entry
|
|
359
|
+
# in **pydna.ini** file or the pydna_cached_funcs environment variable.
|
|
367
360
|
|
|
368
|
-
|
|
369
|
-
|
|
361
|
+
# """
|
|
362
|
+
# return _open_folder(_os.environ["pydna_config_dir"])
|
|
370
363
|
|
|
371
364
|
|
|
372
|
-
def open_log_folder():
|
|
373
|
-
|
|
374
|
-
|
|
365
|
+
# def open_log_folder():
|
|
366
|
+
# """docstring."""
|
|
367
|
+
# return _open_folder(_os.environ["pydna_log_dir"])
|
|
375
368
|
|
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def get_env():
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message = f.renderText(message)
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return _pretty_str(message)
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if __name__ == "__main__":
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import os as _os
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cached = _os.getenv("pydna_cached_funcs", "")
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_os.environ["pydna_cached_funcs"] = ""
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import doctest
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doctest.testmod(verbose=True, optionflags=doctest.ELLIPSIS)
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_os.environ["pydna_cached_funcs"] = cached
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@@ -7,8 +7,7 @@ for for nicer string output in the IPython shell and Jupyter notebook.
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"""
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from prettytable import PrettyTable as _Pt
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from prettytable import
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from prettytable import TableStyle as _TableStyle
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from copy import copy as _copy
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from typing import List as _List
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@@ -33,16 +32,5 @@ class PrettyTable(_Pt):
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def _repr_markdown_(self) -> pretty_str:
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c = _copy(self)
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c.set_style(
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c.set_style(_TableStyle.MARKDOWN)
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return pretty_str(c.get_string())
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if __name__ == "__main__":
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import os as _os
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cached = _os.getenv("pydna_cached_funcs", "")
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_os.environ["pydna_cached_funcs"] = ""
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import doctest
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doctest.testmod(verbose=True, optionflags=doctest.ELLIPSIS)
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_os.environ["pydna_cached_funcs"] = cached
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@@ -18,10 +18,8 @@ ttt
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Dseqrecord(-3)
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>>> from pydna.all import __all__
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>>> __all__
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['Anneal', 'pcr', 'Assembly', 'genbank', 'Genbank', 'download_text
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', '
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', 'ape', 'primer_design', 'assembly_fragments', 'circular_assembly_fragments\
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', 'eq', 'gbtext_clean', 'PrimerList']
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+
['Anneal', 'pcr', 'Assembly', 'genbank', 'Genbank', 'download_text', 'Dseqrecord',
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+
'Dseq', 'read', 'read_primer', 'parse', 'parse_primers', 'primer_design', 'assembly_fragments', 'eq', 'gbtext_clean']
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>>>
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"""
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@@ -39,13 +37,13 @@ __all__ = [
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"read_primer",
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"parse",
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"parse_primers",
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"ape",
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+
# "ape",
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"primer_design",
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"assembly_fragments",
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-
"circular_assembly_fragments",
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+
# "circular_assembly_fragments",
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"eq",
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"gbtext_clean",
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-
"PrimerList",
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+
# "PrimerList",
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]
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@@ -61,21 +59,13 @@ from pydna.readers import read
|
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from pydna.readers import read_primer
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from pydna.parsers import parse
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from pydna.parsers import parse_primers
|
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-
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+
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+
# from pydna.editor import ape
|
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from pydna.design import primer_design
|
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from pydna.design import assembly_fragments
|
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-
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+
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+
# from pydna.design import circular_assembly_fragments
|
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from pydna.utils import eq
|
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from pydna.genbankfixer import gbtext_clean
|
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|
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from pydna.myprimers import PrimerList
|
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71
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-
|
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-
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if __name__ == "__main__":
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import os as _os
|
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|
-
|
|
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cached = _os.getenv("pydna_cached_funcs", "")
|
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|
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_os.environ["pydna_cached_funcs"] = ""
|
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|
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import doctest
|
|
79
70
|
|
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80
|
-
|
|
81
|
-
_os.environ["pydna_cached_funcs"] = cached
|
|
71
|
+
# from pydna.myprimers import PrimerList
|