pheval-exomiser 0.4.0__tar.gz → 0.4.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/PKG-INFO +1 -1
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/pyproject.toml +1 -1
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/prepare/create_batch_commands.py +11 -7
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/prepare/tool_specific_configuration_options.py +2 -2
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/run/run.py +5 -1
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/README.md +0 -0
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/__init__.py +0 -0
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/cli.py +0 -0
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/constants.py +0 -0
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/post_process/__init__.py +0 -0
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/post_process/post_process.py +0 -0
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/post_process/post_process_results_format.py +0 -0
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/prepare/__init__.py +0 -0
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/prepare/write_application_properties.py +0 -0
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/run/__init__.py +0 -0
- {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/runner.py +0 -0
{pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/prepare/create_batch_commands.py
RENAMED
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@@ -90,6 +90,7 @@ class CommandCreator:
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),
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raw_results_dir=Path(RAW_RESULTS_TARGET_DIRECTORY_DOCKER),
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output_formats=self.output_formats,
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analysis_yaml=self.analysis_yaml,
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)
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elif self.environment == "local":
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return ExomiserCommandLineArguments(
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@@ -98,6 +99,7 @@ class CommandCreator:
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output_options_file=output_options_file,
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raw_results_dir=self.results_dir,
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output_formats=self.output_formats,
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analysis_yaml=self.analysis_yaml,
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)
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raise ValueError(f"Unknown environment: {self.environment}")
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@@ -248,11 +250,14 @@ class CommandsWriter:
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self, command_arguments: ExomiserCommandLineArguments
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) -> None:
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"""Write a phenotype-only command out for exomiser ≥13.2.0 to run."""
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if command_arguments.analysis_yaml is None:
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phenotype_only_statement = (
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" --preset phenotype-only"
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if version.parse(self.exomiser_version) < version.parse("15.0.0")
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else " --preset phenotype_only"
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)
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else:
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phenotype_only_statement = f" --analysis {str(command_arguments.analysis_yaml)}"
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self.file.write(
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"--sample "
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+ str(command_arguments.sample)
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@@ -260,8 +265,7 @@ class CommandsWriter:
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+ str(command_arguments.raw_results_dir)
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+ " --output-filename "
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+ f"{Path(command_arguments.sample).stem}-exomiser"
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+
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+ phenotype_only
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+ phenotype_only_statement
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)
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def write_phenotype_only_command(self, command_arguments: ExomiserCommandLineArguments):
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@@ -1,5 +1,5 @@
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from pathlib import Path
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from typing import List, Optional
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from typing import List, Optional, Union
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from pydantic import BaseModel, Field
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@@ -61,7 +61,7 @@ class ExomiserConfigurations(BaseModel):
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environment: str = Field(...)
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exomiser_software_directory: Path = Field(...)
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analysis_configuration_file: Path = Field(...)
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analysis_configuration_file: Union[Path | None] = Field(...)
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max_jobs: int = Field(...)
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application_properties: ApplicationProperties = Field(...)
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output_formats: Optional[List[str]] = Field(None)
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@@ -40,7 +40,11 @@ def prepare_batch_files(
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config.output_formats.append("JSON")
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create_batch_file(
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environment=config.environment,
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analysis=
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analysis=(
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input_dir.joinpath(config.analysis_configuration_file)
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if config.analysis_configuration_file
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else None
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),
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phenopacket_dir=Path(testdata_dir).joinpath("phenopackets"),
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vcf_dir=vcf_dir_name if variant_analysis else None,
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output_dir=tool_input_commands_dir,
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{pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/post_process/__init__.py
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{pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/post_process/post_process.py
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