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‎.gitignore

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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env/
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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*.egg-info/
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.installed.cfg
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*.egg
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*,cover
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.hypothesis/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# pyenv python configuration file
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.python-version
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.vscode/

‎LICENSE

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GNU GENERAL PUBLIC LICENSE
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Version 3, 29 June 2007
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A simple genome de-replication tool with fastANI
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Copyright (C) 2020 Antonio Fernandez-Guerra
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <http://www.gnu.org/licenses/>.
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Also add information on how to contact you by electronic and paper mail.
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You should also get your employer (if you work as a programmer) or school,
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if any, to sign a "copyright disclaimer" for the program, if necessary.
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For more information on this, and how to apply and follow the GNU GPL, see
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<http://www.gnu.org/licenses/>.
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The GNU General Public License does not permit incorporating your program
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into proprietary programs. If your program is a subroutine library, you
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may consider it more useful to permit linking proprietary applications with
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the library. If this is what you want to do, use the GNU Lesser General
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Public License instead of this License. But first, please read
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<http://www.gnu.org/philosophy/why-not-lgpl.html>.
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‎MANIFEST.in

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include versioneer.py
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include bam_filter/_version.py

‎README.md

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Large diffs are not rendered by default.

‎appveyor.yml

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environment:
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global:
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# SDK v7.0 MSVC Express 2008's SetEnv.cmd script will fail if the
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# /E:ON and /V:ON options are not enabled in the batch script intepreter
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# See: http://stackoverflow.com/a/13751649/163740
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CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\tools\\appveyor\\run_with_env.cmd"
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matrix:
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- PYTHON: "C:\\Miniconda36-x64"
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PYTHON_VERSION: "3.6"
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PYTHON_ARCH: "64"
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- PYTHON: "C:\\Miniconda-x64"
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PYTHON_VERSION: "2.7"
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PYTHON_ARCH: "64"
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init:
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- ECHO %PYTHON% %PYTHON_VERSION% %PYTHON_ARCH% %HOME%
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install:
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# If there is a newer build queued for the same PR, cancel this one.
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# The AppVeyor 'rollout builds' option is supposed to serve the same
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# purpose but it is problematic because it tends to cancel builds pushed
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# directly to master instead of just PR builds (or the converse).
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# credits: JuliaLang developers.
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- ps:
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if ($env:APPVEYOR_PULL_REQUEST_NUMBER -and $env:APPVEYOR_BUILD_NUMBER -ne ((Invoke-RestMethod `
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https://ci.appveyor.com/api/projects/$env:APPVEYOR_ACCOUNT_NAME/$env:APPVEYOR_PROJECT_SLUG/history?recordsNumber=50).builds | `
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Where-Object pullRequestId -eq $env:APPVEYOR_PULL_REQUEST_NUMBER)[0].buildNumber) { `
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throw "There are newer queued builds for this pull request, failing early." }
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# these correspond to folder naming of miniconda installs on appveyor. See
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# https://www.appveyor.com/docs/installed-software#python
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- if "%PYTHON_VERSION%" == "3.6" set "BASE_PYTHON_VERSION=36"
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- if "%PYTHON_ARCH%" == "64" set "ARCH_LABEL=-x64"
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- call "C:\Miniconda%BASE_PYTHON_VERSION%%ARCH_LABEL%\Scripts\activate.bat"
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- conda config --set always_yes yes
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- conda update -q conda
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- conda config --set auto_update_conda no
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- conda update -q --all
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- conda install -q pytest pytest-cov conda-build anaconda-client
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- conda info
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# this is to ensure dependencies
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- conda build conda.recipe --no-test
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- conda install --use-local bam_filter
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# Not a .NET project, we build package in the install step instead
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build: false
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test_script:
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- py.test --color=yes -v --cov bam_filter --cov-report xml tests
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on_success:
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- conda install -c conda-forge codecov
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- codecov --env PYTHON_VERSION --file C:\projects\bam-filter\coverage.xml

‎bam_filter/__init__.py

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from ._version import get_versions
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__version__ = get_versions()["version"]
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del get_versions

‎bam_filter/__main__.py

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"""
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This program is free software: you can redistribute it and/or modify it under the terms of the GNU
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General Public License as published by the Free Software Foundation, either version 3 of the
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License, or (at your option) any later version.
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This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
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even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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General Public License for more details.
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You should have received a copy of the GNU General Public License along with this program. If not,
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see <https://www.gnu.org/licenses/>.
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"""
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import logging
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from bam_filter.sam_utils import processBam, filterReferenceBAMfile
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from bam_filter.utils import (
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get_arguments,
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)
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log = logging.getLogger("my_logger")
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def main():
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logging.basicConfig(
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level=logging.DEBUG, format="%(levelname)s ::: %(asctime)s ::: %(message)s"
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)
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args = get_arguments()
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logging.getLogger("my_logger").setLevel(
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logging.DEBUG if args.debug else logging.INFO
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)
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datadf = processBam(bam=args.bam, threads=args.threads)
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datadf_filtered = datadf.loc[
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(datadf["breadthExpRatio"] > args.breadthExpRatio)
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& (datadf["covEvenness"] > args.covEvenness)
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& (datadf["nReads"] > args.nReads)
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]
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datadf.to_csv(args.output, sep="\t", index=False)
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refs_dict = dict(zip(datadf["chromosome"], datadf["referenceLength"]))
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filterReferenceBAMfile(args.bam, refs_dict, outBAMfile="test.bam")
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if __name__ == "__main__":
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main()

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