Closed YingYa closed 4 months ago
Hi,
I run SigProfilerAssignment (v0.1.6) using Command Line Interface, but failed to set "collapse_to_SBS96 = False".
SigProfilerAssignment cosmic_fit --genome_build GRCh38 --cosmic_version 3.4 --collapse_to_SBS96 False --input_type matrix --context_type 48 --export_probabilities_per_mutation True Cancer.CNV48.matrix.tsv COSMIC_fitting_cnv/
-------Python and Package Versions------- Python Version: 3.9.19 SigProfilerPlotting Version: 1.3.23 SigProfilerMatrixGenerator Version: 1.2.26 SigProfilerAssignment Version: 0.1.6 Pandas version: 1.5.3 Numpy version: 1.25.2
--------------EXECUTION PARAMETERS-------------- INPUT DATA input_type: matrix output: COSMIC_fitting_cnv/ samples: Cancer.CNV48.matrix.tsv reference_genome: GRCh38 context_types: 48 exome: False COSMIC MATCH cosmic_version: 3.4 nnls_add_penalty: 0.05 nnls_remove_penalty: 0.01 initial_remove_penalty: 0.05 de_novo_fit_penalty: 0.02 export_probabilities: True collapse_to_SBS96: True denovo_refit_option: False decompose_fit_option: False cosmic_fit_option: True
Hi @YingYa,
Thanks for trying out the CLI and identifying this issue with how arguments are handled. We will address this in the upcoming release.
Hi,
I run SigProfilerAssignment (v0.1.6) using Command Line Interface, but failed to set "collapse_to_SBS96 = False".
SigProfilerAssignment cosmic_fit --genome_build GRCh38 --cosmic_version 3.4 --collapse_to_SBS96 False --input_type matrix --context_type 48 --export_probabilities_per_mutation True Cancer.CNV48.matrix.tsv COSMIC_fitting_cnv/
-------Python and Package Versions------- Python Version: 3.9.19 SigProfilerPlotting Version: 1.3.23 SigProfilerMatrixGenerator Version: 1.2.26 SigProfilerAssignment Version: 0.1.6 Pandas version: 1.5.3 Numpy version: 1.25.2
--------------EXECUTION PARAMETERS-------------- INPUT DATA input_type: matrix output: COSMIC_fitting_cnv/ samples: Cancer.CNV48.matrix.tsv reference_genome: GRCh38 context_types: 48 exome: False COSMIC MATCH cosmic_version: 3.4 nnls_add_penalty: 0.05 nnls_remove_penalty: 0.01 initial_remove_penalty: 0.05 de_novo_fit_penalty: 0.02 export_probabilities: True collapse_to_SBS96: True denovo_refit_option: False decompose_fit_option: False cosmic_fit_option: True