pheval-exomiser 0.4.0__py3-none-any.whl → 0.4.1__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-0.4.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pheval_exomiser
-Version: 0.4.0
+Version: 0.4.1
 Summary: 
 Author: Yasemin Bridges
 Author-email: y.bridges@qmul.ac.uk

{pheval_exomiser-0.4.0.dist-info → pheval_exomiser-0.4.1.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-0.4.1.dist-info/METADATA,sha256=p1MedWTLr9ajT7yqQm1PWEl5jrEsGZTZmudOOSHqFiI,7692
+pheval_exomiser-0.4.1.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+pheval_exomiser-0.4.1.dist-info/entry_points.txt,sha256=lbZMu-x7ns8UrFveWSqEQ1UB5l33TbRMomqBUyGYIwI,131
+pheval_exomiser-0.4.1.dist-info/RECORD,,