pheval-exomiser 0.4.0__py3-none-any.whl → 0.4.2__py3-none-any.whl

pheval_exomiser/prepare/create_batch_commands.py

@@ -90,6 +90,7 @@ class CommandCreator:
                 ),
                 raw_results_dir=Path(RAW_RESULTS_TARGET_DIRECTORY_DOCKER),
                 output_formats=self.output_formats,
+                analysis_yaml=self.analysis_yaml,
             )
         elif self.environment == "local":
             return ExomiserCommandLineArguments(
@@ -98,6 +99,7 @@ class CommandCreator:
                 output_options_file=output_options_file,
                 raw_results_dir=self.results_dir,
                 output_formats=self.output_formats,
+                analysis_yaml=self.analysis_yaml,
             )
         raise ValueError(f"Unknown environment: {self.environment}")
 
@@ -248,11 +250,14 @@ class CommandsWriter:
         self, command_arguments: ExomiserCommandLineArguments
     ) -> None:
         """Write a phenotype-only command out for exomiser ≥13.2.0 to run."""
-        phenotype_only = (
-            "phenotype-only"
-            if version.parse(self.exomiser_version) < version.parse("15.0.0")
-            else "phenotype_only"
-        )
+        if command_arguments.analysis_yaml is None:
+            phenotype_only_statement = (
+                " --preset phenotype-only"
+                if version.parse(self.exomiser_version) < version.parse("15.0.0")
+                else " --preset phenotype_only"
+            )
+        else:
+            phenotype_only_statement = f" --analysis {str(command_arguments.analysis_yaml)}"
         self.file.write(
             "--sample "
             + str(command_arguments.sample)
@@ -260,8 +265,7 @@ class CommandsWriter:
             + str(command_arguments.raw_results_dir)
             + " --output-filename "
             + f"{Path(command_arguments.sample).stem}-exomiser"
-            + " --preset "
-            + phenotype_only
+            + phenotype_only_statement
         )
 
     def write_phenotype_only_command(self, command_arguments: ExomiserCommandLineArguments):

pheval_exomiser/prepare/tool_specific_configuration_options.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import List, Optional
+from typing import List, Optional, Union
 
 from pydantic import BaseModel, Field
 
@@ -61,7 +61,7 @@ class ExomiserConfigurations(BaseModel):
 
     environment: str = Field(...)
     exomiser_software_directory: Path = Field(...)
-    analysis_configuration_file: Path = Field(...)
+    analysis_configuration_file: Union[Path | None] = Field(...)
     max_jobs: int = Field(...)
     application_properties: ApplicationProperties = Field(...)
     output_formats: Optional[List[str]] = Field(None)

pheval_exomiser/run/run.py

@@ -40,7 +40,11 @@ def prepare_batch_files(
             config.output_formats.append("JSON")
     create_batch_file(
         environment=config.environment,
-        analysis=input_dir.joinpath(config.analysis_configuration_file),
+        analysis=(
+            input_dir.joinpath(config.analysis_configuration_file)
+            if config.analysis_configuration_file
+            else None
+        ),
         phenopacket_dir=Path(testdata_dir).joinpath("phenopackets"),
         vcf_dir=vcf_dir_name if variant_analysis else None,
         output_dir=tool_input_commands_dir,

{pheval_exomiser-0.4.0.dist-info → pheval_exomiser-0.4.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pheval_exomiser
-Version: 0.4.0
+Version: 0.4.2
 Summary: 
 Author: Yasemin Bridges
 Author-email: y.bridges@qmul.ac.uk
@@ -24,7 +24,7 @@ Description-Content-Type: text/markdown
 
 # Exomiser Runner for PhEval
 
-This is the Exomiser plugin for PhEval. With this plugin, you can leverage the variant prioritisation tool, Exomiser, to run the PhEval pipeline seamlessly. Detailed documentation on how to set up and run the PhEval Makefile pipeline with the Exomiser runner can be found [here](https://monarch-initiative.github.io/pheval/exomiser_pipeline/). The setup process for running the full PhEval Makefile pipeline differs from setting up for a single run. The Makefile pipeline creates directory structures for corpora and configurations to handle multiple run configurations. Detailed instructions on setting up the appropriate directory layout, including the input directory and test data directory, can be found here.
+This is the Exomiser plugin for PhEval. With this plugin, you can leverage the variant prioritisation tool, Exomiser, to run the PhEval pipeline seamlessly. Instructions for setting up the appropriate directory layout, including the input directory and test data directory for a single PhEval run, can be found here.
 
 ## Installation
 

{pheval_exomiser-0.4.0.dist-info → pheval_exomiser-0.4.2.dist-info}/RECORD

@@ -5,13 +5,13 @@ pheval_exomiser/post_process/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NM
 pheval_exomiser/post_process/post_process.py,sha256=bGNLO0LlsG26oKtvL3mtlcBTDY5gynKh1BwNjmUaIgI,972
 pheval_exomiser/post_process/post_process_results_format.py,sha256=Y5Wi6zkBUaDoHVqFD5tmToGLSEqc86hN5s08edL4Tic,12287
 pheval_exomiser/prepare/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pheval_exomiser/prepare/create_batch_commands.py,sha256=g3hTCWDldqD0oLmIoZeinLn9uS2ZX2Hm6jqTxvATf8I,18638
-pheval_exomiser/prepare/tool_specific_configuration_options.py,sha256=4gedZ9iadRXK6tF9P-ju-dhj8-F2-fhrXVhfYIsAxFQ,2922
+pheval_exomiser/prepare/create_batch_commands.py,sha256=G-2pRboJalW8MeXDwSHR1ZAuhNdQJdHjJPxOo0KBgPM,18930
+pheval_exomiser/prepare/tool_specific_configuration_options.py,sha256=pFzieoZogiPhSquN2p7THcXuCBrzqANwqbWO0e6BPu4,2943
 pheval_exomiser/prepare/write_application_properties.py,sha256=KmG7GvkQo8AhnhRyqohTFvqjfhEhbcs78UYYoigxJ3w,8933
 pheval_exomiser/run/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pheval_exomiser/run/run.py,sha256=yyjjNgOOm1baDFWwQ2ENU4YeHtIOnvaQ7b3DmWtb7zY,7934
+pheval_exomiser/run/run.py,sha256=n9cDv9E4d-NELCIY_v2UCrXqbWOo27TM2_9lPn-YOwI,8030
 pheval_exomiser/runner.py,sha256=RqVobVJlOwcPzbO5gLjDtkGaygWdFT9VrlIvOmyBQPw,2706
-pheval_exomiser-0.4.0.dist-info/METADATA,sha256=7fNZcLql69hJXVZr2XA3znjVp8O5s__FIHdCV6lu4A0,7692
-pheval_exomiser-0.4.0.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-pheval_exomiser-0.4.0.dist-info/entry_points.txt,sha256=lbZMu-x7ns8UrFveWSqEQ1UB5l33TbRMomqBUyGYIwI,131
-pheval_exomiser-0.4.0.dist-info/RECORD,,
+pheval_exomiser-0.4.2.dist-info/METADATA,sha256=vTvN9EASW_2YxWqZ4hQhWGIRIJtRMq_vTsEhTHR7h8g,7294
+pheval_exomiser-0.4.2.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+pheval_exomiser-0.4.2.dist-info/entry_points.txt,sha256=lbZMu-x7ns8UrFveWSqEQ1UB5l33TbRMomqBUyGYIwI,131
+pheval_exomiser-0.4.2.dist-info/RECORD,,