From 826fdc9c6acf526f7968c27aa5fec822806ea8bb Mon Sep 17 00:00:00 2001 From: Miles Smith Date: Fri, 14 Jul 2023 15:22:02 -0500 Subject: [PATCH] python 3.10, dep updates, move to hatchling --- .github/workflows/build.yml | 2 +- .pre-commit-config.yaml | 2 +- CHANGELOG.md | 10 + LICENSE | 27 - LICENSE.md | 595 ++++++++++++++++ README.md | 2 +- poetry.lock | 1268 --------------------------------- pyproject.toml | 219 +++--- setup.cfg | 2 +- src/plinkliftover/__init__.py | 46 +- src/plinkliftover/__main__.py | 141 ++-- src/plinkliftover/bed2map.py | 59 +- src/plinkliftover/liftover.py | 63 +- src/plinkliftover/logger.py | 94 +-- src/plinkliftover/map2bed.py | 61 +- 15 files changed, 935 insertions(+), 1656 deletions(-) delete mode 100755 LICENSE create mode 100755 LICENSE.md delete mode 100644 poetry.lock diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index ac734c5..c05b408 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -7,7 +7,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.8"] + python-version: ["3.10"] steps: - uses: actions/checkout@v3.3.0 diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a5f6686..7b368c1 100755 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,5 +1,5 @@ default_language_version: - python: python3.8 + python: python3.10 default_stages: [commit, push] diff --git a/CHANGELOG.md b/CHANGELOG.md index 0bcff85..c926b12 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,16 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [0.4.0] - 2023-07-13 + +### Change + +- Update dependencies +- Adjust functions to use updated `typer` syntax +- Increase required python version to 3.10 +- Switch from using `poetry` to `hatchling`/`huak` + + ## [0.3.0] - 2022-02-17 ### Added diff --git a/LICENSE b/LICENSE deleted file mode 100755 index dab65fe..0000000 --- a/LICENSE +++ /dev/null @@ -1,27 +0,0 @@ -Copyright (c) 2013, - -All rights reserved. - -Redistribution and use in source and binary forms, with or without modification, -are permitted provided that the following conditions are met: - - * Redistributions of source code must retain the above copyright notice, - this list of conditions and the following disclaimer. - * Redistributions in binary form must reproduce the above copyright notice, - this list of conditions and the following disclaimer in the documentation - and/or other materials provided with the distribution. - * Neither the name of lice nor the names of its contributors - may be used to endorse or promote products derived from this software - without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS -"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT -LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR -A PARTICULAR PURPOSE ARE DISCLAIMED. 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No Surrender of Others' Freedom + +If conditions are imposed on you (whether by court order, agreement or otherwise) +that contradict the conditions of this License, they do not excuse you from the +conditions of this License. If you cannot convey a covered work so as to satisfy +simultaneously your obligations under this License and any other pertinent +obligations, then as a consequence you may not convey it at all. For example, if you +agree to terms that obligate you to collect a royalty for further conveying from +those to whom you convey the Program, the only way you could satisfy both those terms +and this License would be to refrain entirely from conveying the Program. + +### 13. Use with the GNU Affero General Public License + +Notwithstanding any other provision of this License, you have permission to link or +combine any covered work with a work licensed under version 3 of the GNU Affero +General Public License into a single combined work, and to convey the resulting work. +The terms of this License will continue to apply to the part which is the covered +work, but the special requirements of the GNU Affero General Public License, section +13, concerning interaction through a network will apply to the combination as such. + +### 14. Revised Versions of this License + +The Free Software Foundation may publish revised and/or new versions of the GNU +General Public License from time to time. Such new versions will be similar in spirit +to the present version, but may differ in detail to address new problems or concerns. + +Each version is given a distinguishing version number. If the Program specifies that +a certain numbered version of the GNU General Public License “or any later +version” applies to it, you have the option of following the terms and +conditions either of that numbered version or of any later version published by the +Free Software Foundation. If the Program does not specify a version number of the GNU +General Public License, you may choose any version ever published by the Free +Software Foundation. + +If the Program specifies that a proxy can decide which future versions of the GNU +General Public License can be used, that proxy's public statement of acceptance of a +version permanently authorizes you to choose that version for the Program. + +Later license versions may give you additional or different permissions. However, no +additional obligations are imposed on any author or copyright holder as a result of +your choosing to follow a later version. + +### 15. Disclaimer of Warranty + +THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. +EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES +PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER +EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE +QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE +DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + +### 16. Limitation of Liability + +IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY +COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS +PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, +INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE +PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE +OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE +WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE +POSSIBILITY OF SUCH DAMAGES. + +### 17. Interpretation of Sections 15 and 16 + +If the disclaimer of warranty and limitation of liability provided above cannot be +given local legal effect according to their terms, reviewing courts shall apply local +law that most closely approximates an absolute waiver of all civil liability in +connection with the Program, unless a warranty or assumption of liability accompanies +a copy of the Program in return for a fee. + +_END OF TERMS AND CONDITIONS_ + +## How to Apply These Terms to Your New Programs + +If you develop a new program, and you want it to be of the greatest possible use to +the public, the best way to achieve this is to make it free software which everyone +can redistribute and change under these terms. + +To do so, attach the following notices to the program. It is safest to attach them +to the start of each source file to most effectively state the exclusion of warranty; +and each file should have at least the “copyright” line and a pointer to +where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + +If the program does terminal interaction, make it output a short notice like this +when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type 'show c' for details. + +The hypothetical commands `show w` and `show c` should show the appropriate parts of +the General Public License. Of course, your program's commands might be different; +for a GUI interface, you would use an “about box”. + +You should also get your employer (if you work as a programmer) or school, if any, to +sign a “copyright disclaimer” for the program, if necessary. For more +information on this, and how to apply and follow the GNU GPL, see +<>. + +The GNU General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may consider it +more useful to permit linking proprietary applications with the library. If this is +what you want to do, use the GNU Lesser General Public License instead of this +License. But first, please read +<>. diff --git a/README.md b/README.md index 39e8b8a..17256f3 100755 --- a/README.md +++ b/README.md @@ -19,7 +19,7 @@ another. ## Installation PLINKLiftOver requires -* Python 3.8 +* Python 3.10 * The command line version of [liftOver](http://genome.ucsc.edu/cgi-bin/hgLiftOver), installed and on the system path * An appropriate [chain file](http://hgdownload.soe.ucsc.edu/downloads.html#liftover) diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 5e33936..0000000 --- a/poetry.lock +++ /dev/null @@ -1,1268 +0,0 @@ -[[package]] -name = "astroid" -version = "2.9.3" -description = "An abstract syntax tree for Python with inference support." -category = "dev" -optional = false -python-versions = ">=3.6.2" - -[package.dependencies] -lazy-object-proxy = ">=1.4.0" -setuptools = ">=20.0" -typing-extensions = {version = ">=3.10", markers = "python_version < \"3.10\""} -wrapt = ">=1.11,<1.14" - -[[package]] -name = "atomicwrites" -version = "1.4.0" -description = "Atomic file writes." -category = "dev" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" - -[[package]] -name = "attrs" -version = "21.4.0" -description = "Classes Without Boilerplate" -category = "dev" -optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" - -[package.extras] -dev = ["cloudpickle", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "mypy", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "sphinx", "sphinx-notfound-page", "zope.interface"] -docs = ["furo", "sphinx", "sphinx-notfound-page", "zope.interface"] -tests = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six", "zope.interface"] -tests_no_zope = ["cloudpickle", "coverage[toml] (>=5.0.2)", "hypothesis", "mypy", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "six"] - -[[package]] -name = "bandit" -version = "1.7.2" -description = "Security oriented static analyser for python code." -category = "dev" -optional = false -python-versions = ">=3.7" - -[package.dependencies] -colorama = {version = ">=0.3.9", markers = "platform_system == \"Windows\""} -GitPython = ">=1.0.1" -PyYAML = ">=5.3.1" -stevedore = ">=1.20.0" - -[package.extras] -test = ["beautifulsoup4 (>=4.8.0)", "coverage (>=4.5.4)", "fixtures (>=3.0.0)", "flake8 (>=4.0.0)", "pylint (==1.9.4)", "stestr (>=2.5.0)", "testscenarios (>=0.5.0)", "testtools (>=2.3.0)", "toml"] -toml = ["toml"] -yaml = ["PyYAML"] - -[[package]] -name = "black" -version = "21.12b0" -description = "The uncompromising code formatter." -category = "dev" -optional = false -python-versions = ">=3.6.2" - -[package.dependencies] -click = ">=7.1.2" -mypy-extensions = ">=0.4.3" -pathspec = ">=0.9.0,<1" -platformdirs = ">=2" -tomli = ">=0.2.6,<2.0.0" -typing-extensions = [ - {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}, - {version = ">=3.10.0.0,<3.10.0.1 || >3.10.0.1", markers = "python_version >= \"3.10\""}, -] - -[package.extras] -colorama = ["colorama (>=0.4.3)"] -d = ["aiohttp (>=3.7.4)"] -jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"] -python2 = ["typed-ast (>=1.4.3)"] -uvloop = ["uvloop (>=0.15.2)"] - -[[package]] -name = "certifi" -version = "2021.10.8" -description = "Python package for providing Mozilla's CA Bundle." -category = "dev" -optional = false -python-versions = "*" - -[[package]] -name = "cfgv" -version = "3.3.1" -description = "Validate configuration and produce human readable error messages." -category = "dev" -optional = false -python-versions = ">=3.6.1" - -[[package]] -name = "charset-normalizer" -version = "2.0.12" -description = "The Real First Universal Charset Detector. 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-# Keywords description https://python-poetry.org/docs/pyproject/#keywords -keywords = [] # Update me - -# Pypi classifiers: https://pypi.org/classifiers/ -classifiers = [ # Update me - "Development Status :: 3 - Alpha", - "Intended Audience :: Developers", - "Operating System :: OS Independent", - "Topic :: Software Development :: Libraries :: Python Modules", +dependencies = [ + "psutil ==5.9.5", + "rich ==13.4.2", + "typer ==0.9.0", + "loguru ==0.7.0", ] -[tool.poetry.scripts] -# Entry points for the package https://python-poetry.org/docs/pyproject/#scripts -"plinkliftover" = "plinkliftover.__main__:app" -"map2bed"= "plinkliftover.map2bed:map2bedapp" -"bed2map"= "plinkliftover.bed2map:bed2mapapp" +[[project.authors]] +name = "Miles Smith" +email = "miles-smith@omrf.org" -[tool.poetry.dependencies] -python = ">=3.8.3,<4.0" -typer = "^0.4.0" -rich = "^10.2.1" -psutil = "^5.8.0" +[project.urls] +repository = "https://github.com/milescsmith/plinkliftover" +homepage = "https://github.com/milescsmith/plinkliftover" -[tool.poetry.dev-dependencies] -darglint = "^1.5.8" -isort = "^5.7.0" -pyupgrade = "^2.17" -black = "^21.12b0" -mypy = "0.921" -bandit = "^1.7.0" -safety = "^1.10.3" -pytest = "^6.2" -pylint = "^2.8.2" -pydocstyle = "^6.1.1" -pre-commit = "^2.12.1" -flakehell = "^0.9.0" -flake8-broken-line = "^0.6.0" -flake8-bugbear = "^21.4" -flake8-builtins = "^1.5.3" -flake8-comprehensions = "^3.5.0" -flake8-eradicate = "^1.0.0" -flake8-isort = "^4.0.0" -pycodestyle = "^2.6.0" -pyflakes = "^2.2.0" +[project.scripts] +plinkliftover = "plinkliftover.__main__:app" +map2bed = "plinkliftover.map2bed:map2bedapp" +bed2map = "plinkliftover.bed2map:bed2mapapp" -[tool.black] -# https://github.com/psf/black -line-length = 80 -target-version = ["py38"] +[project.optional-dependencies] +dev = [ + "bandit ==1.7.5", + "black ==23.7.0", + "darglint ==1.8.1", + "flakehell ==0.9.0", + "isort ==5.12.0", + "jupyterlab ==4.0.3", + "mypy ==1.4.1", + "nox ==2023.4.22", + "pre-commit ==3.3.3", + "pycodestyle ==2.10.0", + "pydocstyle ==6.3.0", + "pyflakes ==3.0.1", + "pylint ==2.17.4", + "pytest ==7.4.0", + "pyupgrade ==3.9.0", + "safety ==2.3.4", +] [tool.isort] -# https://github.com/timothycrosley/isort/ known_typing = "typing,types,typing_extensions,mypy,mypy_extensions" sections = "FUTURE,TYPING,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER" include_trailing_comma = true @@ -78,48 +65,86 @@ force_grid_wrap = 0 use_parentheses = true line_length = 80 +[tool.hatch.build.targets.wheel] +packages = ["src/plinkliftover"] -[tool.flakehell] -# optionally inherit from remote config (or local if you want) -base = "https://raw.githubusercontent.com/life4/flakehell/master/pyproject.toml" -# specify any flake8 options. For example, exclude "example.py": -exclude = ["example.py"] -# make output nice -# format = "grouped" -# 80 chars aren't enough in 21 century -max_line_length = 90 -# show line of source code in output -show_source = true +[tool.black] +line-length = 120 +target-version = ["py310"] +skip-string-normalization = true -[tool.flakehell.plugins] -flake8-bandit = ["+*"] -flake8-bugbear = ["-B950"] -flake8-builtins = ["+*"] -pylint = ["+*", "-C0103", "-C0116", "-C901", "-E203", "-E401", "-E501", "-E266", "-F401", "-F403", "-R0913", "-R0914", "-W503", "-W1203", "-W1309"] -# wemake-python-styleguide = ["+*", "-WPS305", "-WPS221", "-WPS111", "-WPS231", "-WPS326", "-WPS337", "-WPS336", "-WPS528", "-WPS529"] -flake8-broken-line = ["+*"] -flake8-commas = ["+*"] -flake8-comprehensions = ["+*"] -# flake8-darglint = ["+*", "-DAR101"] -flake8-debugger = ["+*"] -# flake8-docstrings = ["+*"] -flake8-eradicate = ["+*", "-E800"] -flake8-isort = ["+*"] -# flake8-rst-docstrings = ["+*"] -# flake8-string-format = ["+*"] -# mccabe = ["+*"] -# pep8-naming = ["+*"] -pycodestyle = ["+*","-E203", "-E401", "-E501", "-E266", "-W503", "-W1203", "-W1309"] -pyflakes = ["+*"] +[tool.ruff] +target-version = "py310" +line-length = 120 +select = [ + "A", + "ARG", + "B", + "C", + "DTZ", + "E", + "EM", + "F", + "FBT", + "I", + "I001", + "ICN", + "ISC", + "N", + "PLC", + "PLE", + "PLR", + "PLW", + "Q", + "RUF", + "S", + "T", + "TID", + "UP", + "W", + "YTT", +] +ignore = [ + "B027", + "FBT003", + "S105", + "S106", + "S107", + "C901", + "PLR0911", + "PLR0912", + "PLR0913", + "PLR0915", +] +unfixable = [ + "F401", + "UP007", +] +exclude = [ + ".git", + ".hg", + "__pycache__", + "_bin/*", + "_build/*", + "_ig_fbcode_wheel/*", + "buck-out/*", + "third-party-buck/*", + "third-party2/*", + "dist", + ".venv", + ".nox", + ".mypy_cache", + ".pytype", + ".svn", + "__pypackages__", +] +src = ["src"] -# match by prefix -[tool.flakehell.exceptions."tests/"] -pycodestyle = ["-*"] # disable a check -pyflakes = ["-*"] # disable a plugin +[tool.ruff.mccabe] +max-complexity = 50 -[tool.flakehell.exceptions."tests/test_example.py"] -pyflakes = ["+*"] # enable a plugin +[tool.ruff.isort] +known-first-party = ["readcounts"] -# match by glob -[tool.flakehell.exceptions."**/test_*.py"] -pyflakes = ["-*"] +[tool.ruff.flake8-tidy-imports] +ban-relative-imports = "all" diff --git a/setup.cfg b/setup.cfg index a82165c..b45aae9 100755 --- a/setup.cfg +++ b/setup.cfg @@ -10,7 +10,7 @@ docstring_style = google [mypy] # mypy configurations: http://bit.ly/2zEl9WI -python_version = 3.7 +python_version = 3.10 pretty = True allow_redefinition = False check_untyped_defs = True diff --git a/src/plinkliftover/__init__.py b/src/plinkliftover/__init__.py index 23680b2..dcb2f6a 100755 --- a/src/plinkliftover/__init__.py +++ b/src/plinkliftover/__init__.py @@ -1,6 +1,11 @@ -# type: ignore[attr-defined] -"""`plinkliftover` Converts genotype data stored in plink's PED+MAP format from one genome build to another, using liftOver""" +""" +`plinkliftover` Converts genotype data stored in plink's PED+MAP +format from one genome build to another, using liftOver +""" from importlib.metadata import PackageNotFoundError, version +from typing import Annotated + +from loguru import logger try: __version__ = version(__name__) @@ -11,19 +16,38 @@ from rich.console import Console console = Console() +logger.disable("readcounts") + +app = typer.Typer( + name="plinkliftover", + help="Converts genotype data stored in plink's PED+MAP format from one genome build to another, using liftOver", + add_completion=False, +) + +verbosity_level = 0 -def version_callback(value: bool): +def version_callback(value: bool) -> None: # noqa FBT001 """Prints the version of the package.""" if value: - console.print( - f"[yellow]plinkliftover[/] version: [bold blue]{__version__}[/]" - ) + console.print(f"[yellow]plinkliftover[/] version: [bold blue]{__version__}[/]") raise typer.Exit() -app = typer.Typer( - name="plinkliftover", - help="Converts genotype data stored in plink's PED+MAP format from one genome build to another, using liftOver", - add_completion=False, -) +@app.callback() +def verbosity( + verbose: Annotated[ + int, + typer.Option( + "-v", + "--verbose", + help="Control output verbosity. Pass this argument multiple times to increase the amount of output.", + count=True, + ), + ] = 0 +) -> None: + verbosity_level = verbose # noqa: F841 + + +if __name__ == "main": + app() diff --git a/src/plinkliftover/__main__.py b/src/plinkliftover/__main__.py index 90a9312..b8e99cd 100755 --- a/src/plinkliftover/__main__.py +++ b/src/plinkliftover/__main__.py @@ -1,50 +1,57 @@ -# type: ignore[attr-defined] -from typing import Optional - from distutils.spawn import find_executable from pathlib import Path +from typing import Annotated, Optional import typer +from loguru import logger -from . import __version__, app, console, version_callback -from .bed2map import bed2map -from .liftover import liftBed, liftDat, liftPed -from .logger import plo_logger as logger -from .map2bed import map2bed +from plinkliftover import app, console, verbosity_level, version_callback +from plinkliftover.bed2map import bed2map +from plinkliftover.liftover import lift_bed, lift_dat, lift_ped +from plinkliftover.logger import init_logger +from plinkliftover.map2bed import map2bed -@app.command(name="") +@app.command(name="liftover") def liftover( - mapfile: str = typer.Argument( - ..., help="The plink MAP file to `liftOver`." - ), - chainfile: str = typer.Argument( - ..., help="The location of the chain files to provide to `liftOver`." - ), - pedfile: Optional[str] = typer.Option( - None, - help='Optionally remove "unlifted SNPs" from the plink PED file after running `liftOver`.', - show_default=False, - ), - datfile: Optional[str] = typer.Option( - None, - help="Optionally remove 'unlifted SNPs' from a data file containing a list of SNPs (e.g. for --exclude or --include in `plink`)", - show_default=False, - ), - prefix: Optional[str] = typer.Option( - None, help="The prefix to give to the output files.", show_default=False - ), - liftoverexecutable: Optional[str] = typer.Option( - None, help="The location of the `liftOver` executable." - ), - version: bool = typer.Option( - None, - "-v", - "--version", - callback=version_callback, - is_eager=True, - help="Prints the version of the plinkliftover package.", - ), + mapfile: Annotated[ + Path, + typer.Argument(help="The plink MAP file to `liftOver`."), + ], + chainfile: Annotated[Path, typer.Argument(help="The location of the chain files to provide to `liftOver`.")], + pedfile: Annotated[ + Optional[Path], # noqa UP007 + typer.Option( + help='Optionally remove "unlifted SNPs" from the plink PED file after running `liftOver`.', + show_default=False, + ), + ] = None, + datfile: Annotated[ + Optional[Path], # noqa UP007 + typer.Option( + help=( + "Optionally remove 'unlifted SNPs' from a data file containing a list of SNPs " + "(e.g. for --exclude or --include in `plink`)" + ), + show_default=False, + ), + ] = None, + prefix: Annotated[ + Optional[str], typer.Option(help="The prefix to give to the output files.", show_default=False) # noqa UP007 + ] = None, + liftoverexecutable: Annotated[ + Optional[str], typer.Option(help="The location of the `liftOver` executable.") # noqa UP007 + ] = None, + version: Annotated[ # noqa ARG007 + bool, + typer.Option( + "-V", + "--version", + callback=version_callback, + is_eager=True, + help="Prints the version of the plinkliftover package.", + ), + ] = False, # noqa FBT002 ) -> None: """Converts genotype data stored in plink's PED+MAP format from one genome build to another, using liftOver. @@ -52,36 +59,33 @@ def liftover( # Show usage message if user hasn't provided any arguments, rather # than giving a non-descript error message with the usage() - mapfile = Path(mapfile) + init_logger(verbose=verbosity_level) + oldbed = mapfile.with_suffix(".bed") map2bed(mapfile, oldbed) # If a location is not specified for the liftOver executable. # assume it is in the User's $PATH. if liftoverexecutable is None: - try: - liftOverPath = Path(find_executable("liftOver")) - except TypeError as e: - logger.exception( - "The `liftOver` executable was not found. Please make sure it is installed and in the PATH" - ) - logger.error(e) + if (lop := find_executable("liftOver")) is not None: + lift_over_path = Path(lop) + if not lift_over_path.exists(): + msg = "The `liftOver` executable was not found. Please make sure it is installed and in the PATH" + logger.exception(msg) + raise FileNotFoundError(msg) else: - liftOverPath = Path(liftoverexecutable) - if not liftOverPath.exists(): - logger.exception( - "The `liftOver` executable was not found. Please make sure it is installed and in the PATH" - ) - raise FileNotFoundError( - "The `liftOver` executable was not found. Please make sure it is installed and in the PATH" - ) + lift_over_path = Path(liftoverexecutable) + if not lift_over_path.exists(): + msg = "The `liftOver` executable was not found. Please make sure it is installed and in the PATH" + logger.exception(msg) + raise FileNotFoundError(msg) newbed = Path(f"{mapfile}.bed") - lifted_set, unlifted_set, lb_status = liftBed( + lifted_set, unlifted_set, lb_status = lift_bed( fin=oldbed, fout=newbed, chainfile=chainfile, - liftOverPath=liftOverPath, + lift_over_path=lift_over_path, ) if lb_status: @@ -99,9 +103,7 @@ def liftover( console.print(f"[pink]{datfile.name}[/]") newdat = Path(f"{prefix}.dat") - ld_status = liftDat(fin=datfile, fout=newdat, lifted_set=lifted_set) - - if ld_status: + if lift_dat(fin=datfile, fout=newdat, lifted_set=lifted_set): console.print("lifting [purple]dat[/] file: [green]SUCCESS[/]") logger.info(f"lifting map file: {newmap} - SUCCESS") else: @@ -111,27 +113,16 @@ def liftover( if pedfile is not None: pedfile = Path(pedfile) console.print(f"[pink]{pedfile.name}[/]") - newPed = Path(f"{prefix}.ped") - lp_status = liftPed( - fin=pedfile, fout=newPed, fOldMap=mapfile, unlifted_set=unlifted_set - ) + new_ped = Path(f"{prefix}.ped") - if lp_status: - console.print( - "lifting [dark_orange3]ped[/] file: [bold green]SUCCESS[/]" - ) + if lift_ped(fin=pedfile, fout=new_ped, foldmap=mapfile, unlifted_set=unlifted_set): + console.print("lifting [dark_orange3]ped[/] file: [bold green]SUCCESS[/]") logger.info("lifting ped file: SUCCESS") else: - console.print( - "lifting [dark_orange3]ped[/] file: [bold red]FAILED[/]" - ) + console.print("lifting [dark_orange3]ped[/] file: [bold red]FAILED[/]") logger.info("lifting ped file: FAILED") console.print("cleaning up BED files...") logger.info("cleaning up BED files...") newbed.unlink() oldbed.unlink() - - -if __name__ == "__main__": - typer.run(main) diff --git a/src/plinkliftover/bed2map.py b/src/plinkliftover/bed2map.py index b103078..92078ad 100644 --- a/src/plinkliftover/bed2map.py +++ b/src/plinkliftover/bed2map.py @@ -1,29 +1,26 @@ -from typing import Optional - from pathlib import Path +from typing import Annotated, Optional import typer +from loguru import logger -from . import app, console, version_callback -from .logger import plo_logger as logger +from plinkliftover import app, console, verbosity_level, version_callback +from plinkliftover.logger import init_logger -# bed2mapapp = typer.Typer( -# name="bed2map", -# help="Converts BED files to PLINK MAP format", -# add_completion=False, -# ) +BED_LINES_LENGTH: int = 4 def bed2map(fin: Path, fout: Path) -> bool: + init_logger(verbosity_level) logger.info(f"fin: {fin}, fout: {fout}") console.print( f"Converting lifted [green]BED[/] [blue]{fin.name}[/] file back to [green]MAP[/] [yellow]{fout.name}[/]..." ) lines = fin.read_text().split("\n") - output = list() + output = [] with typer.progressbar(lines) as bed_lines: for line in bed_lines: - if len(x := line.split()) == 4: + if len(x := line.split()) == BED_LINES_LENGTH: chrom, _, pos1, rs = x chrom = chrom.replace("chr", "") output.append(f"{chrom}\t{rs}\t0.0\t{pos1}") @@ -33,23 +30,29 @@ def bed2map(fin: Path, fout: Path) -> bool: @app.command(name="bed2map") def bed2mapapp( - bedfile: Path = typer.Argument(..., help="A BED file."), - output: Optional[Path] = typer.Option( - None, - "-o", - "--output", - help=f"Location to save MAP file to. If one is not provided, " - f"then it will be saved to where the BED file is.", - show_default=True, - ), - version: bool = typer.Option( - None, - "-v", - "--version", - callback=version_callback, - is_eager=True, - help="Prints the version of the plinkliftover package.", - ), + bedfile: Annotated[Path, typer.Argument(help="A BED file.")], + output: Annotated[ + Optional[Path], # noqa UP007 + typer.Option( + "-o", + "--output", + help=( + "Location to save MAP file to. If one is not provided, " + "then it will be saved to where the BED file is." + ), + show_default=True, + ), + ] = None, + version: Annotated[ # noqa ARG001 + Optional[bool], # noqa UP007 + typer.Option( + "-v", + "--version", + callback=version_callback, + is_eager=True, + help="Prints the version of the plinkliftover package.", + ), + ] = None, ) -> None: """Convert genotype data stored in a PLINK MAP file into a BED file, allowing one to use the online version of liftOver should the local diff --git a/src/plinkliftover/liftover.py b/src/plinkliftover/liftover.py index 873e14f..a3427d4 100755 --- a/src/plinkliftover/liftover.py +++ b/src/plinkliftover/liftover.py @@ -14,98 +14,85 @@ - to generally be slightly more PEP compliant. Modified by Miles Smith: - - Update to work with python >=3.7 + - Update to work with python >= 3.10 """ -from typing import Set, Tuple - import sys from pathlib import Path from subprocess import check_output +from loguru import logger from typer import progressbar -from . import console -from .logger import plo_logger as logger +from plinkliftover import console + +DAT_LINE_LENGTH: int = 2 -def liftBed( +def lift_bed( fin: Path, fout: Path, chainfile: Path, - liftOverPath: Path, -) -> Tuple[Set[str]]: + lift_over_path: Path, +) -> tuple[set[str], set[str], bool]: console.print(f"Lifting [green]BED[/] file [blue]{fin.name}[/]...") - params = { - "LIFTOVER_BIN": liftOverPath.resolve(), + params: dict[str, str | Path] = { + "LIFTOVER_BIN": lift_over_path.resolve(), "OLD": fin, "CHAIN": chainfile, "NEW": fout, "UNLIFTED": f"{fout}.unlifted", } - check_output(params.values()) + check_output([str(params[_]) for _ in params]) # noqa: S603 # record lifted/unliftd rs unlifted_lines = Path(params["UNLIFTED"]).read_text().split("\n") console.print(f"Processing [red]unlifted[/] {fout.name}.unlifted") with progressbar(unlifted_lines) as unlifted: - unlifted_set = { - ln.strip().split()[-1] - for ln in unlifted - if len(ln) > 0 and ln[0] != "#" - } + unlifted_set = {ln.strip().split()[-1] for ln in unlifted if len(ln) > 0 and ln[0] != "#"} console.print(f"Processing [red]new[/] {fout.name}") new_bed_lines = Path(params["NEW"]).read_text().split("\n") with progressbar(new_bed_lines) as new_bed: - lifted_set = { - ln.strip().split()[-1] - for ln in new_bed - if len(ln) != 0 and ln[0] != "#" - } + lifted_set = {ln.strip().split()[-1] for ln in new_bed if len(ln) != 0 and ln[0] != "#"} return lifted_set, unlifted_set, True -def liftDat(fin: Path, fout: Path, lifted_set: Set[str]) -> bool: +def lift_dat(fin: Path, fout: Path, lifted_set: set[str]) -> bool: console.print(f"Updating [green]DAT[/] file [pink]{fin.name}[/]...") lines = fin.read_text().split("\n") - output = list() + output = [] with progressbar(lines) as dat_lines: for ln in dat_lines: if len(ln) == 0 or ln[0] != "M": output.append(ln) - else: - if len(thing := ln.strip().split()) == 2: - _, rs = thing - if rs in lifted_set: - output.append(ln) + elif len(thing := ln.strip().split()) == DAT_LINE_LENGTH: + _, rs = thing + if rs in lifted_set: + output.append(ln) console.print(f"Writing [green]new DAT[/] file [pink]{fout.name}[/]...") return True -def liftPed( - fin: Path, fout: Path, fOldMap: Path, unlifted_set: Set[str] -) -> bool: +def lift_ped(fin: Path, fout: Path, foldmap: Path, unlifted_set: set[str]) -> bool: # two ways to do it: # 1. write unlifted snp list # use PLINK to do this job using --exclude # 2. alternatively, we can write our own method # we will use method 2 - marker = [i.strip().split()[1] for i in open(fOldMap)] + marker = [i.strip().split()[1] for i in open(foldmap)] flag = [(x not in unlifted_set) for x in marker] console.print(f"Updating [green]PED[/] file [orange]{fin.resolve()}[/]...") lines = fin.read_text().split("\n") - output = list() + output = [] with progressbar(lines) as liftped_lines: for ln in liftped_lines: if ln.strip() != "": f = ln.strip().split() - f = f[:6] + [ - f[i * 2] + " " + f[i * 2 + 1] for i in range(3, len(f) // 2) - ] + f = f[:6] + [f"{f[i * 2]} {f[i * 2 + 1]}" for i in range(3, len(f) // 2)] if len(f[6:]) != len(flag): logger.error("Inconsistent length of ped and map files") logger.error(f"{len(f[6:])} vs {len(flag)}") @@ -115,9 +102,7 @@ def liftPed( a = "\t".join(f[:6]) b = "\t".join(newmarker) output.append(f"{a}\t{b}\n") - console.print( - f"Writing new [green]PED[/] data to [light_slate_blue]{fout.resolve()}[/]" - ) + console.print(f"Writing new [green]PED[/] data to [light_slate_blue]{fout.resolve()}[/]") with open(fout, "w") as fo: fo.writelines(output) return True diff --git a/src/plinkliftover/logger.py b/src/plinkliftover/logger.py index 62f8f7e..e90b274 100755 --- a/src/plinkliftover/logger.py +++ b/src/plinkliftover/logger.py @@ -1,82 +1,22 @@ -# stolen wholesale from `anndata `_ -# BSD 3-Clause License +import datetime +from sys import stderr -# Copyright (c) 2017-2018 P. Angerer, F. Alexander Wolf, Theis Lab -# All rights reserved. +from loguru import logger -# Redistribution and use in source and binary forms, with or without -# modification, are permitted provided that the following conditions are met: -# * Redistributions of source code must retain the above copyright notice, this -# list of conditions and the following disclaimer. +def init_logger(verbose: int, msg_format: str | None = None) -> None: + if msg_format is None: + msg_format = "{name}:{function}:{line}·-·{message}" -# * Redistributions in binary form must reproduce the above copyright notice, -# this list of conditions and the following disclaimer in the documentation -# and/or other materials provided with the distribution. + timezone = datetime.datetime.now(datetime.timezone.utc).astimezone().tzinfo + logger.add(f"readcounts_{datetime.datetime.now(tz=timezone).strftime('%d-%m-%Y--%H-%M-%S')}.log", level="DEBUG") -# * Neither the name of the copyright holder nor the names of its -# contributors may be used to endorse or promote products derived from -# this software without specific prior written permission. - -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE -# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE -# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL -# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR -# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER -# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, -# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -import logging -import os - -_previous_memory_usage = None - -plo_logger = logging.getLogger("plinkliftover") -# Don’t pass log messages on to logging.root and its handler -plo_logger.propagate = False -plo_logger.setLevel("ERROR") -plo_logger.addHandler(logging.StreamHandler()) # Logs go to stderr -plo_logger.handlers[-1].setFormatter(logging.Formatter("%(message)s")) -plo_logger.handlers[-1].setLevel("ERROR") - - -def get_logger(name): - """\ - Creates a child logger that delegates to plo_logger - instead to logging.root - """ - return plo_logger.manager.getLogger(name) - - -def get_memory_usage(): - import psutil - - process = psutil.Process(os.getpid()) - try: - meminfo = process.memory_info() - except AttributeError: - meminfo = process.get_memory_info() - mem = meminfo[0] / 2 ** 30 # output in GB - mem_diff = mem - global _previous_memory_usage - if _previous_memory_usage is not None: - mem_diff = mem - _previous_memory_usage - _previous_memory_usage = mem - return mem, mem_diff - - -def format_memory_usage(mem_usage, msg="", newline=False): - newline = "\n" if newline else "" - more = " \n... " if msg != "" else "" - mem, diff = mem_usage - return ( - f"{newline}{msg}{more}" - f"Memory usage: current {mem:.2f} GB, difference {diff:+.2f} GB" - ) - - -def print_memory_usage(msg="", newline=False): - print(format_memory_usage(get_memory_usage(), msg, newline)) + match verbose: + case 3: + logger.add(stderr, format=msg_format, level="DEBUG") + case 2: + logger.add(stderr, format=msg_format, level="INFO") + case 1: + logger.add(stderr, format=msg_format, level="WARNING") + case _: + logger.add(stderr, format=msg_format, level="ERROR") diff --git a/src/plinkliftover/map2bed.py b/src/plinkliftover/map2bed.py index 8ee65ad..2492ab9 100644 --- a/src/plinkliftover/map2bed.py +++ b/src/plinkliftover/map2bed.py @@ -1,17 +1,13 @@ -from typing import Optional - from pathlib import Path +from typing import Annotated, Optional import typer +from loguru import logger -from . import app, console, version_callback -from .logger import plo_logger as logger +from plinkliftover import app, console, verbosity_level, version_callback +from plinkliftover.logger import init_logger -# map2bedapp = typer.Typer( -# name="map2bed", -# help="Converts PLINK MAP files into BED format", -# add_completion=False, -# ) +MAP_LINE_LENGTH: int = 4 def map2bed(fin: Path, fout: Path) -> bool: @@ -19,38 +15,43 @@ def map2bed(fin: Path, fout: Path) -> bool: console.print( f"Converting [green]MAP[/] file [yellow]{fin.name}[/] file to [green]UCSC BED[/] file [blue]{fout.name}[/]..." ) + init_logger(verbosity_level) lines = fin.read_text().split("\n") - output = list() + output = [] with typer.progressbar(lines) as map_lines: for line in map_lines: - if len(x := line.split()) == 4: + if len(x := line.split()) == MAP_LINE_LENGTH: chrom, rs, _, pos = x output.append(f"chr{chrom}\t{int(pos)-1}\t{int(pos)}\t{rs}") - else: - pass fout.write_text("\n".join(output)) return True @app.command(name="map2bed") def map2bedapp( - mapfile: Path = typer.Argument(..., help="A PLINK MAP file."), - output: Optional[Path] = typer.Option( - None, - "-o", - "--output", - help=f"Location to save BED file to. If one is not provided, " - f"then it will be saved to where the MAP file is.", - show_default=True, - ), - version: bool = typer.Option( - None, - "-v", - "--version", - callback=version_callback, - is_eager=True, - help="Prints the version of the plinkliftover package.", - ), + mapfile: Annotated[Path, typer.Argument(help="A PLINK MAP file.")], + output: Annotated[ + Optional[Path], # noqa UP007 + typer.Option( + "-o", + "--output", + help=( + "Location to save BED file to. If one is not provided, " + "then it will be saved to where the MAP file is." + ), + show_default=True, + ), + ] = None, + version: Annotated[ # noqa ARG001 + bool, + typer.Option( + "-v", + "--version", + callback=version_callback, + is_eager=True, + help="Prints the version of the plinkliftover package.", + ), + ] = False, # noqa FBT007 ) -> None: """Convert genotype data stored in a PLINK MAP file into a BED file, allowing one to use the online version of liftOver should the local