Merge pull request #60 from monarch-initiative/59-allow-for-multiple-…

…output-formats-from-exomiser

59 allow for multiple output formats from exomiser

README.md

@@ -42,6 +42,7 @@ tool_specific_configuration_options:
     phenotype_data_version: 2302
     cache_type:
     cache_caffeine_spec:
+  output_formats: [JSON,HTML] # options include HTML, JSON, TSV_VARIANT, TSV_GENE, VCF
   post_process:
     score_name: combinedScore
     sort_order: DESCENDING

config.yaml

@@ -22,6 +22,7 @@ tool_specific_configuration_options:
     # either none, simple, or caffeine
     cache_type: none
     cache_caffeine_spec:
+  output_formats: JSON # can be HTML, JSON, TSV_VARIANT, TSV_GENE, VCF
   post_process:
     # For Exomiser, valid ranking methods include combinedScore, priorityScore, variantScore or pValue
     score_name: combinedScore

src/pheval_exomiser/prepare/create_batch_commands.py

@@ -1,8 +1,7 @@
-#!/usr/bin/python
 import tempfile
 from dataclasses import dataclass
 from pathlib import Path
-from typing import Optional
+from typing import List, Optional
 
 import click
 from phenopackets import Family, Phenopacket
@@ -30,9 +29,10 @@ class ExomiserCommandLineArguments:
     raw_results_dir: Path or None = None
     variant_analysis: bool or None = None
     output_options_file: Optional[Path] = None
+    output_formats: List[str] or None = None
 
 
-def get_all_files_from_output_opt_directory(output_options_dir: Path) -> list[Path] or None:
+def get_all_files_from_output_opt_directory(output_options_dir: Path) -> List[Path] or None:
     """Obtain all output options files if directory is specified - otherwise returns none."""
     return None if output_options_dir is None else all_files(output_options_dir)
 
@@ -46,10 +46,11 @@ def __init__(
         phenopacket_path: Path,
         phenopacket: Phenopacket or Family,
         variant_analysis: bool,
-        output_options_dir_files: list[Path] or None,
+        output_options_dir_files: List[Path] or None,
         output_options_file: Path or None,
         raw_results_dir: Path or None,
         analysis_yaml: Path or None,
+        output_formats: List[str] or None,
     ):
         self.environment = environment
         self.phenopacket_path = phenopacket_path
@@ -59,6 +60,7 @@ def __init__(
         self.output_options_file = output_options_file
         self.results_dir = raw_results_dir
         self.analysis_yaml = analysis_yaml
+        self.output_formats = output_formats
 
     def assign_output_options_file(self) -> Path or None:
         """Return the path of a single output option yaml if specified,
@@ -86,13 +88,15 @@ def add_phenotype_only_arguments(self) -> ExomiserCommandLineArguments:
                     else None
                 ),
                 raw_results_dir=RAW_RESULTS_TARGET_DIRECTORY_DOCKER,
+                output_formats=self.output_formats,
             )
         elif self.environment == "local":
             return ExomiserCommandLineArguments(
                 sample=Path(self.phenopacket_path),
                 variant_analysis=self.variant_analysis,
                 output_options_file=output_options_file,
                 raw_results_dir=self.results_dir,
+                output_formats=self.output_formats,
             )
 
     def add_variant_analysis_arguments(self, vcf_dir: Path) -> ExomiserCommandLineArguments:
@@ -109,6 +113,7 @@ def add_variant_analysis_arguments(self, vcf_dir: Path) -> ExomiserCommandLineAr
                 variant_analysis=self.variant_analysis,
                 raw_results_dir=self.results_dir,
                 analysis_yaml=self.analysis_yaml,
+                output_formats=self.output_formats,
             )
         elif self.environment == "docker":
             return ExomiserCommandLineArguments(
@@ -143,7 +148,8 @@ def create_command_arguments(
     output_options_dir: Path or None = None,
     output_options_file: Path or None = None,
     analysis_yaml: Path or None = None,
-) -> list[ExomiserCommandLineArguments]:
+    output_formats: List[str] or None = None,
+) -> List[ExomiserCommandLineArguments]:
     """Return a list of Exomiser command line arguments for a directory of phenopackets."""
     phenopacket_paths = files_with_suffix(phenopacket_dir, ".json")
     commands = []
@@ -160,6 +166,7 @@ def create_command_arguments(
                 output_options_file,
                 results_dir,
                 analysis_yaml,
+                output_formats,
             ).add_command_line_arguments(vcf_dir)
         )
     return commands
@@ -212,10 +219,22 @@ def write_output_options(self, command_arguments: ExomiserCommandLineArguments)
         except IOError:
             print("Error writing ", self.file)
 
+    def write_output_format(self, command_arguments: ExomiserCommandLineArguments) -> None:
+        """Write output formats for Exomiser raw result output."""
+        try:
+            (
+                self.file.write(" --output-format " + ",".join(command_arguments.output_formats))
+                if command_arguments.output_formats is not None
+                else None
+            )
+        except IOError:
+            print("Error writing ", self.file)
+
     def write_analysis_command(self, command_arguments: ExomiserCommandLineArguments):
         self.write_basic_analysis_command(command_arguments)
         self.write_results_dir(command_arguments)
         self.write_output_options(command_arguments)
+        self.write_output_format(command_arguments)
         self.file.write("\n")
 
     def write_basic_phenotype_only_command(
@@ -239,6 +258,7 @@ def write_basic_phenotype_only_command(
     def write_phenotype_only_command(self, command_arguments: ExomiserCommandLineArguments):
         self.write_basic_phenotype_only_command(command_arguments)
         self.write_output_options(command_arguments)
+        self.write_output_format(command_arguments)
         self.file.write("\n")
 
     def write_local_commands(self, command_arguments: ExomiserCommandLineArguments):
@@ -261,7 +281,7 @@ class BatchFileWriter:
 
     def __init__(
         self,
-        command_arguments_list: list[ExomiserCommandLineArguments],
+        command_arguments_list: List[ExomiserCommandLineArguments],
         variant_analysis: bool,
         output_dir: Path,
         batch_prefix: str,
@@ -326,6 +346,7 @@ def create_batch_file(
     results_dir: Path,
     output_options_dir: Path = None,
     output_options_file: Path = None,
+    output_formats: List[str] = None,
 ) -> None:
     """Create Exomiser batch files."""
     command_arguments = create_command_arguments(
@@ -337,6 +358,7 @@ def create_batch_file(
         output_options_dir,
         output_options_file,
         analysis,
+        output_formats,
     )
     (
         BatchFileWriter(

src/pheval_exomiser/prepare/tool_specific_configuration_options.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+from typing import List
 
 from pydantic import BaseModel, Field
 
@@ -54,6 +55,7 @@ class ExomiserConfigurations(BaseModel):
         analysis_configuration_file (Path): The file name of the analysis configuration file located in the input_dir
         max_jobs (int): Maximum number of jobs to run in a batch
         application_properties (ApplicationProperties): application.properties configurations
+        output_formats: List(str): List of raw output formats.
         post_process (PostProcessing): Post-processing configurations
     """
 
@@ -62,4 +64,5 @@ class ExomiserConfigurations(BaseModel):
     analysis_configuration_file: Path = Field(...)
     max_jobs: int = Field(...)
     application_properties: ApplicationProperties = Field(...)
+    output_formats: List[str] = Field(None)
     post_process: PostProcessing = Field(...)

src/pheval_exomiser/run/run.py

@@ -31,6 +31,11 @@ def prepare_batch_files(
     """Prepare the exomiser batch files"""
     print("...preparing batch files...")
     vcf_dir_name = Path(testdata_dir).joinpath("vcf")
+    output_formats = (
+        config.output_formats + ["JSON"]
+        if config.output_formats and "JSON" not in config.output_formats
+        else config.output_formats
+    )
     create_batch_file(
         environment=config.environment,
         analysis=input_dir.joinpath(config.analysis_configuration_file),
@@ -43,6 +48,7 @@ def prepare_batch_files(
         output_options_dir=None,
         results_dir=raw_results_dir,
         variant_analysis=variant_analysis,
+        output_formats=output_formats,
     )
 
 

tests/test_create_batch_commands.py

@@ -140,6 +140,7 @@ def setUpClass(cls) -> None:
             output_options_file=None,
             raw_results_dir=Path("/path/to/results_dir"),
             analysis_yaml=Path("/path/to/exomiser_analysis.yaml"),
+            output_formats=["JSON"],
         )
         cls.command_creator_output_options_file = CommandCreator(
             environment="local",
@@ -152,6 +153,7 @@ def setUpClass(cls) -> None:
             ),
             raw_results_dir=Path("/path/to/results_dir"),
             analysis_yaml=Path("/path/to/exomiser_analysis.yaml"),
+            output_formats=["JSON"],
         )
         cls.command_creator_none = CommandCreator(
             environment="local",
@@ -162,6 +164,7 @@ def setUpClass(cls) -> None:
             output_options_file=None,
             raw_results_dir=Path("/path/to/results_dir"),
             analysis_yaml=Path("/path/to/exomiser_analysis.yaml"),
+            output_formats=["JSON"],
         )
         cls.command_creator_phenotype_only = CommandCreator(
             environment="local",
@@ -172,6 +175,7 @@ def setUpClass(cls) -> None:
             output_options_file=None,
             raw_results_dir=Path("/path/to/results_dir"),
             analysis_yaml=None,
+            output_formats=["JSON", "HTML"],
         )
         cls.command_creator_phenotype_only_output_options = CommandCreator(
             environment="local",
@@ -184,6 +188,7 @@ def setUpClass(cls) -> None:
             ),
             raw_results_dir=Path("/path/to/results_dir"),
             analysis_yaml=None,
+            output_formats=["JSON"],
         )
 
     def test_assign_output_options_file_from_dir(self):
@@ -210,6 +215,7 @@ def test_add_phenotype_only_arguments(self):
                 vcf_assembly=None,
                 raw_results_dir=Path("/path/to/results_dir"),
                 variant_analysis=False,
+                output_formats=["JSON", "HTML"],
             ),
         )
 
@@ -225,6 +231,7 @@ def test_add_phenotype_only_arguments_output_options(self):
                 output_options_file=Path(
                     "/full/path/to/some/alternate/output_options/phenopacket-output_options.yml"
                 ),
+                output_formats=["JSON"],
             ),
         )
 
@@ -243,6 +250,7 @@ def test_add_variant_analysis_arguments(self):
                     "/full/path/to/some/alternate/output_options/phenopacket-output_options.yml"
                 ),
                 analysis_yaml=Path("/path/to/exomiser_analysis.yaml"),
+                output_formats=["JSON"],
             ),
         )
 
@@ -256,6 +264,7 @@ def test_add_variant_analysis_arguments_none(self):
                 raw_results_dir=Path("/path/to/results_dir"),
                 variant_analysis=False,
                 analysis_yaml=Path("/path/to/exomiser_analysis.yaml"),
+                output_formats=["JSON"],
             ),
         )
 
@@ -274,6 +283,7 @@ def test_add_command_line_arguments(self):
                     "/full/path/to/some/alternate/output_options/phenopacket-output_options.yml"
                 ),
                 analysis_yaml=Path("/path/to/exomiser_analysis.yaml"),
+                output_formats=["JSON"],
             ),
         )
 
@@ -286,5 +296,6 @@ def test_add_command_line_arguments_phenotype_only(self):
                 vcf_assembly=None,
                 raw_results_dir=Path("/path/to/results_dir"),
                 variant_analysis=False,
+                output_formats=["JSON", "HTML"],
             ),
         )

tests/test_write_application_properties.py

@@ -37,6 +37,7 @@ def setUp(cls) -> None:
                     hg19_whitelist_path="2302_hg19_clinvar_whitelist.tsv.gz",
                     hg38_whitelist_path="2302_hg38_clinvar_whitelist.tsv.gz",
                 ),
+                output_formats=["JSON"],
                 post_process=PostProcessing(score_name="combinedScore", sort_order="descending"),
             ),
         )