exposed herediclassify_config path and added automatic conversion of …

…herediclass config pejaver

.gitignore

@@ -186,7 +186,7 @@ classified_structural_variants
 /src/frontend_celery/playwright/redis*
 /Python-*
 /data_makefile
-/.localpython
+/.localpython*
 
 resources/backups/keycloak_export/dev/*/*-users*.json
 /resources/backups/database_dumper/dev/data

src/annotation_service/annotation_jobs/automatic_classification_job.py

@@ -65,8 +65,7 @@ def save_to_db(self, variant_id, conn: Connection):
         if autoclass_input is None:
             return 0, "Not enough information to calculate the automatic classification"
 
-        config_path = os.path.join(paths.automatic_classification_path, "config_production.yaml")
-        returncode, err_msg, classification = self.run_automatic_classification(autoclass_input, config_path)
+        returncode, err_msg, classification = self.run_automatic_classification(autoclass_input, paths.automatic_classification_config_path)
 
         if returncode != 0:
             raise RuntimeError(err_msg)

src/common/paths.py

@@ -43,6 +43,7 @@ def joinpaths(path, *paths):
     ngs_bits_path = joinpaths(toolsdir, "ngs-bits/bin")
     htslib_path = joinpaths(toolsdir, "htslib")
     automatic_classification_path = joinpaths(toolsdir, "herediclass")
+    automatic_classification_config_path = os.path.join(automatic_classification_path, "config_pejaver_mult_strength_production.yaml") # config_production.yaml
     samtools_path = joinpaths(toolsdir, "samtools/samtools")
 
     # data
@@ -245,6 +246,7 @@ def joinpaths(path, *paths):
     htslib_path = joinpaths(toolsdir, "htslib-1.16")
     samtools_path = joinpaths(toolsdir, "samtools/samtools")
     automatic_classification_path = joinpaths(toolsdir, "herediclass")
+    automatic_classification_config_path = os.path.join(automatic_classification_path, "config_production.yaml")
 
 
     # data

tools/script/install_herediclass_config.sh

@@ -52,5 +52,8 @@ for filename in $gene_sepcific_config_path_production/*.yaml; do
    sed -r -i "s:variant_classification/::g" $filename
 done
 
-
+for filename in $gene_sepcific_config_path_production/pejaver_mult_strength/*.yaml; do
+   sed -r -i "s:/home/katzkean/:$variant_classification_path/:g" $filename
+   sed -r -i "s:variant_classification/::g" $filename
+done