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Apply black automatic formatting
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@mdbarnesUCSD
mdbarnesUCSD committed Jan 24, 2024
1 parent 6c6b61b commit 32b67cc
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Showing 15 changed files with 13,942 additions and 7,148 deletions.
154 changes: 148 additions & 6 deletions SigProfilerAssignment/Analyzer.py
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Original file line number Diff line number Diff line change
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from SigProfilerAssignment import decomposition as decomp

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=3.4, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8,exclude_signature_subgroups=None,exome=False,input_type='matrix',context_type="96",export_probabilities=True, export_probabilities_per_mutation=False):
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,exclude_signature_subgroups=exclude_signature_subgroups,exome=exome,input_type=input_type,context_type=context_type,export_probabilities=export_probabilities, export_probabilities_per_mutation=export_probabilities_per_mutation)

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=3.4, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8,exome=False,input_type='matrix',context_type="96",export_probabilities=True, export_probabilities_per_mutation=False):
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,exome=exome,input_type=input_type,context_type=context_type,export_probabilities=export_probabilities, export_probabilities_per_mutation=export_probabilities_per_mutation)
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=3.4,
make_plots=True,
collapse_to_SBS96=True,
connected_sigs=True,
verbose=False,
devopts=None,
new_signature_thresh_hold=0.8,
exclude_signature_subgroups=None,
exome=False,
input_type="matrix",
context_type="96",
export_probabilities=True,
export_probabilities_per_mutation=False,
):
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,
exclude_signature_subgroups=exclude_signature_subgroups,
exome=exome,
input_type=input_type,
context_type=context_type,
export_probabilities=export_probabilities,
export_probabilities_per_mutation=export_probabilities_per_mutation,
)

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=3.4, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,exclude_signature_subgroups=None,exome=False,input_type='matrix',context_type="96",export_probabilities=True, export_probabilities_per_mutation=False, sample_reconstruction_plots=False):
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,exclude_signature_subgroups=exclude_signature_subgroups,exome=exome,input_type=input_type,context_type=context_type,export_probabilities=export_probabilities, export_probabilities_per_mutation=export_probabilities_per_mutation, sample_reconstruction_plots=sample_reconstruction_plots)

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=3.4,
make_plots=True,
collapse_to_SBS96=True,
connected_sigs=True,
verbose=False,
devopts=None,
new_signature_thresh_hold=0.8,
exome=False,
input_type="matrix",
context_type="96",
export_probabilities=True,
export_probabilities_per_mutation=False,
):
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,
exome=exome,
input_type=input_type,
context_type=context_type,
export_probabilities=export_probabilities,
export_probabilities_per_mutation=export_probabilities_per_mutation,
)


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=3.4,
make_plots=True,
collapse_to_SBS96=True,
connected_sigs=True,
verbose=False,
devopts=None,
exclude_signature_subgroups=None,
exome=False,
input_type="matrix",
context_type="96",
export_probabilities=True,
export_probabilities_per_mutation=False,
sample_reconstruction_plots=False,
):
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,
exclude_signature_subgroups=exclude_signature_subgroups,
exome=exome,
input_type=input_type,
context_type=context_type,
export_probabilities=export_probabilities,
export_probabilities_per_mutation=export_probabilities_per_mutation,
sample_reconstruction_plots=sample_reconstruction_plots,
)
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