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mdbarnesUCSDmdbarnesUCSD
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Add support for CLI and cli_controller
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‎MANIFEST.in‎

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include README.md
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include SigProfilerAssignment/controllers/*
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include SigProfilerAssignment/data/*
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include SigProfilerAssignment/data/Reference_Signatures/GRCh37/*
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include SigProfilerAssignment/data/Reference_Signatures/GRCh38/*

‎SigProfilerAssignment/SigProfilerAssignment_CLI.py‎

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#!/usr/bin/env python3
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import sys
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from SigProfilerAssignment.controllers import cli_controller
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def main_function():
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commands = {
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"decompose_fit": "Perform decomposition fitting on the input samples.",
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"denovo_fit": "Perform de novo fitting on the input samples.",
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"cosmic_fit": "Perform COSMIC fitting on the input samples.",
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}
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if len(sys.argv) < 2 or sys.argv[1].lower() not in commands:
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print_usage(commands)
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sys.exit(1)
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command = sys.argv[1].lower()
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args = sys.argv[2:]
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controller = cli_controller.CliController()
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if command == "decompose_fit":
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controller.dispatch_decompose_fit(args)
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elif command == "denovo_fit":
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controller.dispatch_denovo_fit(args)
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elif command == "cosmic_fit":
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controller.dispatch_cosmic_fit(args)
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def print_usage(commands):
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"""Prints the usage message."""
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print("Usage: SigProfilerAssignment <command> [<args>]\n")
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print("Commands:")
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for cmd, desc in commands.items():
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print(f" {cmd}: {desc}")
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if __name__ == "__main__":
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main_function()

‎SigProfilerAssignment/controllers/cli_controller.py‎

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import argparse
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from typing import List
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from SigProfilerAssignment import decomposition as decomp
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def parse_arguments_common(args: List[str], description: str) -> argparse.Namespace:
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parser = argparse.ArgumentParser(description=description)
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parser.add_argument(
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"samples",
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help="Path to the input somatic mutations file (if using segmentation file/mutational matrix) or input folder (mutation calling file/s).",
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)
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parser.add_argument("output", help="Path to the output folder.")
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parser.add_argument(
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"--signatures", help="Path to the signatures file.", default=None
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)
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parser.add_argument(
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"--signature_database",
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help="Path to the signature database file.",
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default=None,
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)
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parser.add_argument(
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"--nnls_add_penalty", type=float, default=0.05, help="NNLS add penalty."
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)
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parser.add_argument(
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"--nnls_remove_penalty", type=float, default=0.01, help="NNLS remove penalty."
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)
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parser.add_argument(
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"--initial_remove_penalty",
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type=float,
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default=0.05,
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help="Initial remove penalty.",
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)
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parser.add_argument(
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"--genome_build",
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default="GRCh37",
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help="The reference genome build (default: GRCh37). Supported genomes: {GRCh37, GRCh38, mm9, mm10, rn6}.",
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)
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parser.add_argument(
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"--cosmic_version",
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type=float,
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default=3.4,
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help="COSMIC version (default: 3.4). Valid options: {1, 2, 3, 3.1, 3.2, 3.3, 3.4}.",
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)
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parser.add_argument(
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"--make_plots", type=bool, default=True, help="Generate plots (default: True)."
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)
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parser.add_argument(
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"--collapse_to_SBS96",
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type=bool,
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default=True,
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help="Collapse to SBS96 (default: True).",
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)
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parser.add_argument(
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"--connected_sigs",
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type=bool,
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default=True,
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help="Connected signatures (default: True).",
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)
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parser.add_argument(
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"--verbose", type=bool, default=False, help="Verbose output (default: False)."
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)
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parser.add_argument(
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"--new_signature_thresh_hold",
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type=float,
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default=0.8,
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help="New signature threshold (default: 0.8).",
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)
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parser.add_argument(
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"--exclude_signature_subgroups",
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default=None,
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help="Remove specific signature subgroups.",
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)
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parser.add_argument(
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"--exome",
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type=bool,
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default=False,
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help="Use exome renormalized COSMIC signatures (default: False).",
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)
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parser.add_argument(
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"--input_type",
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default="matrix",
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help="""Three accepted input types: "vcf", "seg:TYPE", "matrix". Default: "matrix". The accepted callers for TYPE are the following {"ASCAT", "ASCAT_NGS", "SEQUENZA", "ABSOLUTE", "BATTENBERG", "FACETS", "PURPLE", "TCGA"}.""",
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)
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parser.add_argument(
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"--context_type",
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default="96",
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help="""Required context type if `input_type` is "vcf". Valid options: "96", "288", "1536", "DINUC", "ID". Default: "96".""",
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)
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parser.add_argument(
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"--export_probabilities",
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type=bool,
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default=True,
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help="Export probabilities matrix per mutational context (default: True).",
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)
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parser.add_argument(
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"--export_probabilities_per_mutation",
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type=bool,
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default=False,
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help="Export probabilities matrices per mutation (default: False).",
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)
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return parser.parse_args(args)
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class CliController:
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def dispatch_decompose_fit(self, user_args: List[str]) -> None:
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parsed_args = parse_arguments_common(
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user_args, "Perform decomposition fitting on the input samples."
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)
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decomp.spa_analyze(
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samples=parsed_args.samples,
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output=parsed_args.output,
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signatures=parsed_args.signatures,
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signature_database=parsed_args.signature_database,
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nnls_add_penalty=parsed_args.nnls_add_penalty,
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nnls_remove_penalty=parsed_args.nnls_remove_penalty,
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initial_remove_penalty=parsed_args.initial_remove_penalty,
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genome_build=parsed_args.genome_build,
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cosmic_version=parsed_args.cosmic_version,
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make_plots=parsed_args.make_plots,
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collapse_to_SBS96=parsed_args.collapse_to_SBS96,
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connected_sigs=parsed_args.connected_sigs,
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verbose=parsed_args.verbose,
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decompose_fit_option=True,
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denovo_refit_option=False,
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cosmic_fit_option=False,
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new_signature_thresh_hold=parsed_args.new_signature_thresh_hold,
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exclude_signature_subgroups=parsed_args.exclude_signature_subgroups,
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exome=parsed_args.exome,
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input_type=parsed_args.input_type,
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context_type=parsed_args.context_type,
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export_probabilities=parsed_args.export_probabilities,
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export_probabilities_per_mutation=parsed_args.export_probabilities_per_mutation,
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)
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def dispatch_denovo_fit(self, user_args: List[str]) -> None:
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parsed_args = parse_arguments_common(
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user_args, "Perform de novo fitting on the input samples."
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)
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decomp.spa_analyze(
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samples=parsed_args.samples,
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output=parsed_args.output,
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signatures=parsed_args.signatures,
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signature_database=parsed_args.signature_database,
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nnls_add_penalty=parsed_args.nnls_add_penalty,
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nnls_remove_penalty=parsed_args.nnls_remove_penalty,
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initial_remove_penalty=parsed_args.initial_remove_penalty,
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genome_build=parsed_args.genome_build,
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cosmic_version=parsed_args.cosmic_version,
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new_signature_thresh_hold=parsed_args.new_signature_thresh_hold,
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make_plots=parsed_args.make_plots,
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collapse_to_SBS96=parsed_args.collapse_to_SBS96,
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connected_sigs=parsed_args.connected_sigs,
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verbose=parsed_args.verbose,
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decompose_fit_option=False,
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denovo_refit_option=True,
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cosmic_fit_option=False,
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exome=parsed_args.exome,
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input_type=parsed_args.input_type,
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context_type=parsed_args.context_type,
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export_probabilities=parsed_args.export_probabilities,
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export_probabilities_per_mutation=parsed_args.export_probabilities_per_mutation,
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)
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def dispatch_cosmic_fit(self, user_args: List[str]) -> None:
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parsed_args = parse_arguments_common(
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user_args, "Perform COSMIC fitting on the input samples."
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)
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decomp.spa_analyze(
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samples=parsed_args.samples,
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output=parsed_args.output,
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signatures=parsed_args.signatures,
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signature_database=parsed_args.signature_database,
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nnls_add_penalty=parsed_args.nnls_add_penalty,
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nnls_remove_penalty=parsed_args.nnls_remove_penalty,
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initial_remove_penalty=parsed_args.initial_remove_penalty,
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genome_build=parsed_args.genome_build,
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cosmic_version=parsed_args.cosmic_version,
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make_plots=parsed_args.make_plots,
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collapse_to_SBS96=parsed_args.collapse_to_SBS96,
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connected_sigs=parsed_args.connected_sigs,
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verbose=parsed_args.verbose,
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decompose_fit_option=False,
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denovo_refit_option=False,
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cosmic_fit_option=True,
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exclude_signature_subgroups=parsed_args.exclude_signature_subgroups,
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exome=parsed_args.exome,
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input_type=parsed_args.input_type,
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context_type=parsed_args.context_type,
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export_probabilities=parsed_args.export_probabilities,
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export_probabilities_per_mutation=parsed_args.export_probabilities_per_mutation,
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sample_reconstruction_plots=False,
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)

‎setup.py‎

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packages=["SigProfilerAssignment"],
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install_requires=requirements,
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include_package_data=True,
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entry_points={
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"console_scripts": [
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"SigProfilerAssignment=SigProfilerAssignment.SigProfilerAssignment_CLI:main_function",
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],
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},
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zip_safe=False,
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)

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