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U67 #125

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merged 2 commits into from
May 28, 2024
Merged

U67 #125

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a2aa918
Add support for CLI and cli_controller
mdbarnesUCSD May 28, 2024
dfe3628
v0.1.6: Add support for volume parameter and SIGPROFILERASSIGNMENT_VO…
mdbarnesUCSD May 28, 2024
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1 change: 1 addition & 0 deletions MANIFEST.in
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
include README.md
include SigProfilerAssignment/controllers/*
include SigProfilerAssignment/data/*
include SigProfilerAssignment/data/Reference_Signatures/GRCh37/*
include SigProfilerAssignment/data/Reference_Signatures/GRCh38/*
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -68,6 +68,7 @@ Analyze.cosmic_fit(samples, output, input_type="matrix", context_type="96",
| make_plots | Boolean | Toggle on and off for making and saving plots. The default value is True. |
| sample_reconstruction_plots | String | Select the output format for sample reconstruction plots. Valid inputs are {'pdf', 'png', 'both', None}. The default value is None. |
| verbose | Boolean | Prints detailed statements. The default value is False. |
| volume | String | Path to SigProfilerAssignment volumes. Used for Docker/Singularity. Environmental variable "SIGPROFILERASSIGNMENT_VOLUME" takes precedence. Default value is None. |



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6 changes: 6 additions & 0 deletions SigProfilerAssignment/Analyzer.py
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Expand Up @@ -23,6 +23,7 @@ def decompose_fit(
context_type="96",
export_probabilities=True,
export_probabilities_per_mutation=False,
volume=None,
):
decomp.spa_analyze(
samples=samples,
Expand All @@ -49,6 +50,7 @@ def decompose_fit(
context_type=context_type,
export_probabilities=export_probabilities,
export_probabilities_per_mutation=export_probabilities_per_mutation,
volume=volume,
)


Expand All @@ -73,6 +75,7 @@ def denovo_fit(
context_type="96",
export_probabilities=True,
export_probabilities_per_mutation=False,
volume=None,
):
decomp.spa_analyze(
samples=samples,
Expand All @@ -98,6 +101,7 @@ def denovo_fit(
context_type=context_type,
export_probabilities=export_probabilities,
export_probabilities_per_mutation=export_probabilities_per_mutation,
volume=volume,
)


Expand All @@ -123,6 +127,7 @@ def cosmic_fit(
export_probabilities=True,
export_probabilities_per_mutation=False,
sample_reconstruction_plots=False,
volume=None,
):
decomp.spa_analyze(
samples=samples,
Expand All @@ -149,4 +154,5 @@ def cosmic_fit(
export_probabilities=export_probabilities,
export_probabilities_per_mutation=export_probabilities_per_mutation,
sample_reconstruction_plots=sample_reconstruction_plots,
volume=volume,
)
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