adding gene analysis and variant analysis arguments

monarch-initiative · Sep 21, 2023 · 6cb83eb · 6cb83eb
1 parent e0d62db
commit 6cb83eb
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Showing 3 changed files with 25 additions and 17 deletions.
diff --git a/src/pheval_lirical/run/run.py b/src/pheval_lirical/run/run.py
@@ -1,4 +1,3 @@
-import os
 import subprocess
 from pathlib import Path
 
@@ -15,18 +14,12 @@ def prepare_lirical_commands(
     testdata_dir: Path,
     lirical_version: str,
     tool_specific_configurations: LIRICALToolSpecificConfigurations,
+    gene_analysis: bool,
+    variant_analysis: bool,
 ):
     """Write commands to run LIRICAL."""
-    phenopacket_dir = Path(testdata_dir).joinpath(
-        [
-            directory
-            for directory in os.listdir(str(testdata_dir))
-            if "phenopacket" in str(directory)
-        ][0]
-    )
-    vcf_dir = Path(testdata_dir).joinpath(
-        [directory for directory in os.listdir(str(testdata_dir)) if "vcf" in str(directory)][0]
-    )
+    phenopacket_dir = Path(testdata_dir).joinpath("phenopackets")
+    vcf_dir = Path(testdata_dir).joinpath("vcf") if gene_analysis or variant_analysis else None
     prepare_commands(
         lirical_jar=input_dir.joinpath(tool_specific_configurations.lirical_jar_executable),
         input_dir=input_dir.joinpath("data"),
@@ -46,14 +39,15 @@ def prepare_lirical_commands(
             tool_specific_configurations.exomiser_db_configurations.exomiser_hg19_database
         )
         if tool_specific_configurations.exomiser_db_configurations.exomiser_hg19_database
-        is not None
         else None,
         exomiser_hg38_data=input_dir.joinpath(
             tool_specific_configurations.exomiser_db_configurations.exomiser_hg38_database
         )
         if tool_specific_configurations.exomiser_db_configurations.exomiser_hg38_database
         is not None
         else None,
+        gene_analysis=gene_analysis,
+        variant_analysis=variant_analysis,
     ),
 
 

diff --git a/src/pheval_lirical/runner.py b/src/pheval_lirical/runner.py
@@ -37,6 +37,8 @@ def run(self):
             tool_input_commands_dir=self.tool_input_commands_dir,
             lirical_version=self.version,
             tool_specific_configurations=config,
+            gene_analysis=self.input_dir_config.gene_analysis,
+            variant_analysis=self.input_dir_config.variant_analysis,
         )
         run_lirical_local(
             testdata_dir=self.testdata_dir, tool_input_commands_dir=self.tool_input_commands_dir
@@ -53,4 +55,6 @@ def post_process(self):
             output_dir=self.output_dir,
             config=config,
             disease_analysis=self.input_dir_config.disease_analysis,
+            gene_analysis=self.input_dir_config.gene_analysis,
+            variant_analysis=self.input_dir_config.variant_analysis,
         )
diff --git a/tests/test_prepare_commands.py b/tests/test_prepare_commands.py
@@ -211,7 +211,9 @@ def test_get_vcf_assembly(self):
 
     def test_add_manual_cli_arguments(self):
         self.assertEqual(
-            self.command_creator.add_manual_cli_arguments(),
+            self.command_creator.add_manual_cli_arguments(
+                gene_analysis=True, variant_analysis=False
+            ),
             LiricalManualCommandLineArguments(
                 lirical_jar_file=Path("/path/to/lirical.jar"),
                 observed_phenotypes=[
@@ -234,7 +236,9 @@ def test_add_manual_cli_arguments(self):
 
     def test_add_manual_cli_arguments_none_excluded(self):
         self.assertEqual(
-            self.command_creator_none_excluded.add_manual_cli_arguments(),
+            self.command_creator_none_excluded.add_manual_cli_arguments(
+                gene_analysis=True, variant_analysis=False
+            ),
             LiricalManualCommandLineArguments(
                 lirical_jar_file=Path("/path/to/lirical.jar"),
                 observed_phenotypes=[
@@ -259,7 +263,9 @@ def test_add_phenopacket_cli_arguments(self):
         phenopacket_command_creator = copy(self.command_creator)
         phenopacket_command_creator.mode = "phenopacket"
         self.assertEqual(
-            phenopacket_command_creator.add_phenopacket_cli_arguments(),
+            phenopacket_command_creator.add_phenopacket_cli_arguments(
+                gene_analysis=False, variant_analysis=True
+            ),
             LiricalPhenopacketCommandLineArguments(
                 lirical_jar_file=Path("/path/to/lirical.jar"),
                 phenopacket_path=Path("/path/to/phenopacket.json"),
@@ -278,7 +284,9 @@ def test_add_cli_arguments(self):
         phenopacket_command_creator = copy(self.command_creator)
         phenopacket_command_creator.mode = "phenopacket"
         self.assertEqual(
-            phenopacket_command_creator.add_cli_arguments(),
+            phenopacket_command_creator.add_cli_arguments(
+                gene_analysis=True, variant_analysis=True
+            ),
             LiricalPhenopacketCommandLineArguments(
                 lirical_jar_file=Path("/path/to/lirical.jar"),
                 phenopacket_path=Path("/path/to/phenopacket.json"),
@@ -294,7 +302,9 @@ def test_add_cli_arguments(self):
         )
 
         self.assertEqual(
-            self.command_creator_none_excluded.add_cli_arguments(),
+            self.command_creator_none_excluded.add_cli_arguments(
+                gene_analysis=True, variant_analysis=True
+            ),
             LiricalManualCommandLineArguments(
                 lirical_jar_file=Path("/path/to/lirical.jar"),
                 observed_phenotypes=[