diff --git a/besca/datasets/homologs/MGItoHGNC.csv b/besca/datasets/homologs/MGItoHGNC.tsv similarity index 100% rename from besca/datasets/homologs/MGItoHGNC.csv rename to besca/datasets/homologs/MGItoHGNC.tsv diff --git a/besca/datasets/homologs/__init__.py b/besca/datasets/homologs/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/setup.py b/setup.py index 76cc2036..1c5834e2 100644 --- a/setup.py +++ b/setup.py @@ -1,38 +1,44 @@ """ setup procedure """ -if __name__ == '__main__': +if __name__ == "__main__": from setuptools import setup, find_packages import versioneer - reqs = open('requirements.txt', encoding='utf-8').readlines() + reqs = open("requirements.txt", encoding="utf-8").readlines() requires = [req.strip() for req in reqs] with open("README.md", "r") as fh: - long_description = fh.read() + long_description = fh.read() - setup(name='besca', - version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), - description='Collection of BEDA internal python functions for analysing single cell RNAseq data.', - long_description=long_description, - long_description_content_type="text/markdown", - classifiers=[ - 'Development Status :: 5 - Production/Stable', - 'Intended Audience :: Developers', - 'Topic :: Software Development :: Build Tools', - 'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.8'], - url='https://github.com/bedapub/besca', - license='GPLv3', - author='BEDA community', - author_email='manuel.kohler@roche.com', - packages=find_packages(exclude=["devtools", "tests"]), - zip_safe=False, - package_data={'besca.datasets.data': ['*.h5ad'], - 'besca.st': ['*.css'], - 'besca.datasets.nomenclature': ['*.tsv'], - 'besca.datasets.mito_files': ['*.tsv'], - 'besca.datasets.genesets': ['*.gmt', '*.tsv']}, - install_requires=requires) + setup( + name="besca", + version=versioneer.get_version(), + cmdclass=versioneer.get_cmdclass(), + description="Collection of BEDA internal python functions for analysing single cell RNAseq data.", + long_description=long_description, + long_description_content_type="text/markdown", + classifiers=[ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Developers", + "Topic :: Software Development :: Build Tools", + "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.8", + ], + url="https://github.com/bedapub/besca", + license="GPLv3", + author="BEDA community", + author_email="manuel.kohler@roche.com", + packages=find_packages(exclude=["devtools", "tests"]), + zip_safe=False, + package_data={ + "besca.datasets.data": ["*.h5ad"], + "besca.st": ["*.css"], + "besca.datasets.nomenclature": ["*.tsv"], + "besca.datasets.mito_files": ["*.tsv"], + "besca.datasets.genesets": ["*.gmt", "*.tsv"], + "besca.datasets.homologs": ["*.tsv"], + }, + install_requires=requires, + ) diff --git a/workbooks/celltype_annotation_besca.ipynb b/workbooks/celltype_annotation_besca.ipynb index 9b8a246c..a937889a 100644 --- a/workbooks/celltype_annotation_besca.ipynb +++ b/workbooks/celltype_annotation_besca.ipynb @@ -321,7 +321,7 @@ "\n", "if species == \"mouse\":\n", " # Genes converted to mouse homologs\n", - " mousehuman_file = bescapath + \"/besca/datasets/homologs/MGItoHGNC.csv\"\n", + " mousehuman_file = bescapath + \"/besca/datasets/homologs/MGItoHGNC.tsv\"\n", " mousehuman = pd.read_csv(\n", " mousehuman_file, sep=\"\\t\", header=\"infer\", encoding=\"unicode_escape\"\n", " )\n",