From 98b5cb55fd72147e7159120bc9adb7358d0251ab Mon Sep 17 00:00:00 2001
From: Yasemin Bridges <y.bridges@qmul.ac.uk>
Date: Wed, 20 Sep 2023 16:06:01 +0100
Subject: [PATCH] removing specification for output format types

---
 config.yaml                                       |  1 -
 src/pheval_svanna/run/run.py                      | 15 +++------------
 .../tool_specific_configuration_parser.py         |  1 -
 3 files changed, 3 insertions(+), 14 deletions(-)

diff --git a/config.yaml b/config.yaml
index 7f5a136..833fd80 100644
--- a/config.yaml
+++ b/config.yaml
@@ -5,6 +5,5 @@ gene_analysis: False
 disease_analysis: False
 tool_specific_configuration_options:
   svanna_jar_executable: svanna-cli-1.0.3/svanna-cli-1.0.3.jar
-  output_formats: tsv # could be csv,tsv,vcf,html
   post_process:
     sort_order: descending
diff --git a/src/pheval_svanna/run/run.py b/src/pheval_svanna/run/run.py
index 57aa3a6..1e54a44 100644
--- a/src/pheval_svanna/run/run.py
+++ b/src/pheval_svanna/run/run.py
@@ -1,4 +1,3 @@
-import os
 import subprocess
 from pathlib import Path
 
@@ -16,16 +15,8 @@ def prepare_svanna_commands(
     tool_specific_configurations: SvAnnaToolSpecificConfigurations,
 ):
     """Write commands to run SvAnna."""
-    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")
     prepare_commands(
         svanna_jar_file=input_dir.joinpath(tool_specific_configurations.svanna_jar_executable),
         output_dir=tool_input_commands_dir,
@@ -33,7 +24,7 @@ def prepare_svanna_commands(
         phenopacket_dir=phenopacket_dir,
         vcf_dir=vcf_dir,
         results_dir=raw_results_dir,
-        output_format=tool_specific_configurations.output_formats.split(","),
+        output_format="tsv",
         input_data=input_dir,
     )
 
diff --git a/src/pheval_svanna/tool_specific_configuration_parser.py b/src/pheval_svanna/tool_specific_configuration_parser.py
index e00da79..be4fdc7 100644
--- a/src/pheval_svanna/tool_specific_configuration_parser.py
+++ b/src/pheval_svanna/tool_specific_configuration_parser.py
@@ -9,5 +9,4 @@ class PostProcessing(BaseModel):
 
 class SvAnnaToolSpecificConfigurations(BaseModel):
     svanna_jar_executable: Path = Field(...)
-    output_formats: str = Field(...)
     post_process: PostProcessing = Field(...)