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rvangararvangara
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Merge pull request #25 from AlexandrovLab/development
upgrade to v0.0.8
2 parents b16ec45 + 2770a9d commit 9fe5f68

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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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**/.DS_Store
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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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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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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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SigProfilerAssignment/version.py
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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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.nox/
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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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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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test/
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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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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/#use-with-ide
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.pdm.toml
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/

‎README.md‎

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'remove_POL_deficiency_signatures',
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'remove_HR_deficiency_signatures' ,
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'remove_BER_deficiency_signatures',
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'remove_Chemotherapy_signatures',
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'remove_APOBEC_signatures',
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'remove_Tobacco_signatures',
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'remove_UV_signatures',
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'remove_AA_signatures',
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'remove_Colibactin_signatures',
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'remove_Artifact_signatures',
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'remove_Lymphoid_signatures']
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'remove_Chemotherapy_signatures',
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'remove_Immunosuppressants_signatures'
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'remove_Iatrogenic_signatures'
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'remove_APOBEC_signatures',
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'remove_Tobacco_signatures',
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'remove_UV_signatures',
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'remove_AA_signatures',
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'remove_Colibactin_signatures',
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'remove_Artifact_signatures',
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'remove_Lymphoid_signatures']
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```
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|HR_deficiency_signatures| 3|
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|BER_deficiency_signatures| 30, 36|
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|Chemotherapy_signatures| 11, 25, 31, 35, 86, 87, 90|
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|Immunosuppressants_signatures| 32|
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|Iatrogenic_signatures| 11, 25, 31, 32, 35, 86, 87, 90|
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|APOBEC_signatures| 2, 13|
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|Tobacco_signatures |4, 29, 92|
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|UV_signatures| 7a, 7b, 7c, 7d, 38|

‎SigProfilerAssignment/.DS_Store‎

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‎SigProfilerAssignment/Analyzer.py‎

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from SigProfilerAssignment import decomposition as decomp
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def decompose_fit(samples, output, signatures=None, signature_database=None,nnls_add_penalty=0.05, nnls_remove_penalty=0.01, initial_remove_penalty=0.05,genome_build="GRCh37", make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8,signature_subgroups=None):
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def decompose_fit(samples, output, signatures=None, signature_database=None,nnls_add_penalty=0.05, nnls_remove_penalty=0.01, initial_remove_penalty=0.05,genome_build="GRCh37", cosmic_version=3.3, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8,signature_subgroups=None):
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decomp.spa_analyze(samples=samples, output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= True,denovo_refit_option=False,cosmic_fit_option=False,devopts=devopts,new_signature_thresh_hold=new_signature_thresh_hold,signature_subgroups=signature_subgroups)
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decomp.spa_analyze(samples=samples, output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= True,denovo_refit_option=False,cosmic_fit_option=False,devopts=devopts,new_signature_thresh_hold=new_signature_thresh_hold,signature_subgroups=signature_subgroups)
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def denovo_fit(samples, output, signatures=None, signature_database=None,nnls_add_penalty=0.05,nnls_remove_penalty=0.01, initial_remove_penalty=0.05, genome_build="GRCh37", make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8):
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decomp.spa_analyze(samples=samples, output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= False,denovo_refit_option=True,cosmic_fit_option=False,devopts=devopts)
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def denovo_fit(samples, output, signatures=None, signature_database=None,nnls_add_penalty=0.05,nnls_remove_penalty=0.01, initial_remove_penalty=0.05, genome_build="GRCh37", cosmic_version=3.3, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8):
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decomp.spa_analyze(samples=samples, output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, new_signature_thresh_hold=new_signature_thresh_hold, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= False,denovo_refit_option=True,cosmic_fit_option=False,devopts=devopts)
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def cosmic_fit(samples, output, signatures=None, signature_database=None,nnls_add_penalty=0.05, nnls_remove_penalty=0.01, initial_remove_penalty=0.05,genome_build="GRCh37", make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,signature_subgroups=None):
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decomp.spa_analyze(samples=samples, output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= False,denovo_refit_option=False,cosmic_fit_option=True,devopts=devopts,signature_subgroups=signature_subgroups)
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def cosmic_fit(samples, output, signatures=None, signature_database=None,nnls_add_penalty=0.05, nnls_remove_penalty=0.01, initial_remove_penalty=0.05,genome_build="GRCh37", cosmic_version=3.3, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,signature_subgroups=None):
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decomp.spa_analyze(samples=samples, output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= False,denovo_refit_option=False,cosmic_fit_option=True,devopts=devopts,signature_subgroups=signature_subgroups)

‎SigProfilerAssignment/data/.DS_Store‎

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‎SigProfilerAssignment/data/Examples/.DS_Store‎

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‎SigProfilerAssignment/data/Examples/Input_scenario_8/.DS_Store‎

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‎SigProfilerAssignment/data/Examples/Results_scenario_8/.DS_Store‎

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‎SigProfilerAssignment/data/Examples/Results_scenario_8/SBS96/.DS_Store‎

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‎SigProfilerAssignment/data/Examples/Results_scenario_8/SBS96/All_Solutions/.DS_Store‎

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