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.
Files changed (16) hide show
  1. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/PKG-INFO +1 -1
  2. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/pyproject.toml +1 -1
  3. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/prepare/create_batch_commands.py +11 -7
  4. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/prepare/tool_specific_configuration_options.py +2 -2
  5. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/run/run.py +5 -1
  6. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/README.md +0 -0
  7. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/__init__.py +0 -0
  8. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/cli.py +0 -0
  9. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/constants.py +0 -0
  10. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/post_process/__init__.py +0 -0
  11. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/post_process/post_process.py +0 -0
  12. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/post_process/post_process_results_format.py +0 -0
  13. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/prepare/__init__.py +0 -0
  14. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/prepare/write_application_properties.py +0 -0
  15. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/run/__init__.py +0 -0
  16. {pheval_exomiser-0.4.0 → pheval_exomiser-0.4.1}/src/pheval_exomiser/runner.py +0 -0
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: pheval_exomiser
3
- Version: 0.4.0
3
+ Version: 0.4.1
4
4
  Summary:
5
5
  Author: Yasemin Bridges
6
6
  Author-email: y.bridges@qmul.ac.uk
@@ -1,6 +1,6 @@
1
1
  [tool.poetry]
2
2
  name = "pheval_exomiser"
3
- version = "0.4.0"
3
+ version = "0.4.1"
4
4
  description = ""
5
5
  authors = ["Yasemin Bridges <y.bridges@qmul.ac.uk>",
6
6
  "Julius Jacobsen <j.jacobsen@qmul.ac.uk>",
@@ -90,6 +90,7 @@ class CommandCreator:
90
90
  ),
91
91
  raw_results_dir=Path(RAW_RESULTS_TARGET_DIRECTORY_DOCKER),
92
92
  output_formats=self.output_formats,
93
+ analysis_yaml=self.analysis_yaml,
93
94
  )
94
95
  elif self.environment == "local":
95
96
  return ExomiserCommandLineArguments(
@@ -98,6 +99,7 @@ class CommandCreator:
98
99
  output_options_file=output_options_file,
99
100
  raw_results_dir=self.results_dir,
100
101
  output_formats=self.output_formats,
102
+ analysis_yaml=self.analysis_yaml,
101
103
  )
102
104
  raise ValueError(f"Unknown environment: {self.environment}")
103
105
 
@@ -248,11 +250,14 @@ class CommandsWriter:
248
250
  self, command_arguments: ExomiserCommandLineArguments
249
251
  ) -> None:
250
252
  """Write a phenotype-only command out for exomiser ≥13.2.0 to run."""
251
- phenotype_only = (
252
- "phenotype-only"
253
- if version.parse(self.exomiser_version) < version.parse("15.0.0")
254
- else "phenotype_only"
255
- )
253
+ if command_arguments.analysis_yaml is None:
254
+ phenotype_only_statement = (
255
+ " --preset phenotype-only"
256
+ if version.parse(self.exomiser_version) < version.parse("15.0.0")
257
+ else " --preset phenotype_only"
258
+ )
259
+ else:
260
+ phenotype_only_statement = f" --analysis {str(command_arguments.analysis_yaml)}"
256
261
  self.file.write(
257
262
  "--sample "
258
263
  + str(command_arguments.sample)
@@ -260,8 +265,7 @@ class CommandsWriter:
260
265
  + str(command_arguments.raw_results_dir)
261
266
  + " --output-filename "
262
267
  + f"{Path(command_arguments.sample).stem}-exomiser"
263
- + " --preset "
264
- + phenotype_only
268
+ + phenotype_only_statement
265
269
  )
266
270
 
267
271
  def write_phenotype_only_command(self, command_arguments: ExomiserCommandLineArguments):
@@ -1,5 +1,5 @@
1
1
  from pathlib import Path
2
- from typing import List, Optional
2
+ from typing import List, Optional, Union
3
3
 
4
4
  from pydantic import BaseModel, Field
5
5
 
@@ -61,7 +61,7 @@ class ExomiserConfigurations(BaseModel):
61
61
 
62
62
  environment: str = Field(...)
63
63
  exomiser_software_directory: Path = Field(...)
64
- analysis_configuration_file: Path = Field(...)
64
+ analysis_configuration_file: Union[Path | None] = Field(...)
65
65
  max_jobs: int = Field(...)
66
66
  application_properties: ApplicationProperties = Field(...)
67
67
  output_formats: Optional[List[str]] = Field(None)
@@ -40,7 +40,11 @@ def prepare_batch_files(
40
40
  config.output_formats.append("JSON")
41
41
  create_batch_file(
42
42
  environment=config.environment,
43
- analysis=input_dir.joinpath(config.analysis_configuration_file),
43
+ analysis=(
44
+ input_dir.joinpath(config.analysis_configuration_file)
45
+ if config.analysis_configuration_file
46
+ else None
47
+ ),
44
48
  phenopacket_dir=Path(testdata_dir).joinpath("phenopackets"),
45
49
  vcf_dir=vcf_dir_name if variant_analysis else None,
46
50
  output_dir=tool_input_commands_dir,