Rename Notmet and Met prediction statuses

Makefile

@@ -33,35 +33,46 @@ ci-docs-deps:
 
 .PHONY: format
 format:	\
-	format-black \
+	format-ruff \
 	format-isort
 
+.PHONY: format-ruff
+format-ruff:
+	pipenv run ruff format --line-length 100 $(DIRS_PYTHON)
+
 .PHONY: format-isort
 format-isort:
 	pipenv run isort --profile=black --line-length 100 $(DIRS_PYTHON)
 
-.PHONY: format-black
-format-black:
-	pipenv run black --line-length 100 $(DIRS_PYTHON)
+# .PHONY: format-black
+# format-black:
+# 	pipenv run black --line-length 100 $(DIRS_PYTHON)
+
+# .PHONY: format-autoflake
+# format-autoflake:
+# 	pipenv run autoflake --remove-all-unused-imports -i -r $(DIRS_PYTHON)
 
 .PHONY: lint
 lint: \
-	lint-black \
+	lint-ruff \
 	lint-isort \
-	lint-flake8 \
 	lint-mypy
 
+.PHONY: lint-ruff
+lint-ruff:
+	pipenv run ruff check --line-length 100 $(DIRS_PYTHON)
+
 .PHONY: lint-isort
 lint-isort:
 	pipenv run isort --profile=black --line-length 100 --check-only --diff $(DIRS_PYTHON)
 
-.PHONY: lint-black
-lint-black:
-	pipenv run black --check --line-length 100 --diff $(DIRS_PYTHON)
+# .PHONY: lint-black
+# lint-black:
+# 	pipenv run black --check --line-length 100 --diff $(DIRS_PYTHON)
 
-.PHONY: lint-flake8
-flake8:
-	pipenv run flake8 --max-line-length 100 $(DIRS_PYTHON)
+# .PHONY: lint-flake8
+# flake8:
+# 	pipenv run flake8 --max-line-length 100 $(DIRS_PYTHON)
 
 .PHONY: lint-mypy
 lint-mypy:

Pipfile

@@ -22,8 +22,7 @@ typing-extensions = "*"
 datamodel-code-generator = "*"
 debugpy = "*"
 isort = "*"
-flake8 = "*"
-black = "*"
+ruff = "*"
 pytest = "*"
 sphinx = "*"
 sphinxcontrib-bibtex = "*"

src/api/annonars.py

@@ -1,6 +1,6 @@
 """Annonars API client."""
 
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import httpx
 from loguru import logger

src/auto_acmg.py

@@ -1,6 +1,6 @@
 """Implementations of the PVS1 algorithm."""
 
-from typing import Dict, Optional, Type, Union
+from typing import Optional, Type, Union
 
 from loguru import logger
 
@@ -13,14 +13,6 @@
 from src.defs.mehari import CdsPos, ProteinPos, TxPos
 from src.defs.seqvar import SeqVar, SeqVarResolver
 from src.defs.strucvar import StrucVar, StrucVarResolver
-from src.seqvar.auto_bp7 import AutoBP7
-from src.seqvar.auto_pm1 import AutoPM1
-from src.seqvar.auto_pm2_ba1_bs1_bs2 import AutoPM2BA1BS1BS2
-from src.seqvar.auto_pm4_bp3 import AutoPM4BP3
-from src.seqvar.auto_pp2_bp1 import AutoPP2BP1
-from src.seqvar.auto_pp3_bp4 import AutoPP3BP4
-from src.seqvar.auto_ps1_pm5 import AutoPS1PM5
-from src.seqvar.auto_pvs1 import AutoPVS1
 from src.seqvar.default_predictor import DefaultSeqVarPredictor
 from src.strucvar.default_predictor import DefaultStrucVarPredictor
 from src.utils import SeqVarTranscriptsHelper, StrucVarTranscriptsHelper
@@ -86,7 +78,7 @@
     "HGNC:129": CongenitalMyopathiesPredictor,  # ACTA1
     "HGNC:2974": CongenitalMyopathiesPredictor,  # DNM2
     "HGNC:7448": CongenitalMyopathiesPredictor,  # MTM1
-    "HGNC:10483": CongenitalMyopathiesPredictor,  # RYR1
+    # "HGNC:10483": CongenitalMyopathiesPredictor,  # RYR1
     "HGNC:17098": DICER1Predictor,  # DICER1
     "HGNC:1100": ENIGMAPredictor,  # BRCA1
     "HGNC:1101": ENIGMAPredictor,  # BRCA2
@@ -287,7 +279,7 @@ def resolve_variant(self) -> Union[SeqVar, StrucVar, None]:
                     self.variant_name, self.genome_release
                 )
                 return strucvar
-            except ParseError as e:
+            except ParseError:
                 logger.debug("Failed to resolve the structure variant")
                 return None
         except AutoAcmgBaseException as e:

src/bench/comparison_v0.py

@@ -24,7 +24,11 @@
         if record["variant"].startswith("#"):
             continue
         variants.append(
-            (record["variant"], record["expected_criteria"].split(";"), record["comment"])
+            (
+                record["variant"],
+                record["expected_criteria"].split(";"),
+                record["comment"],
+            )
         )
 
 print(f"Number of variants: {len(variants)}")

src/bench/comparison_v1.py

@@ -24,7 +24,11 @@
         if record["variant"].startswith("#"):
             continue
         variants.append(
-            (record["variant"], record["expected_criteria"].split(";"), record["comment"])
+            (
+                record["variant"],
+                record["expected_criteria"].split(";"),
+                record["comment"],
+            )
         )
 
 print(f"Number of variants: {len(variants)}")

src/bench/comparison_v2.py

@@ -58,7 +58,11 @@
         if record["variant"].startswith("#"):
             continue
         variants.append(
-            (record["variant"], record["expected_criteria"].split(";"), record["comment"])
+            (
+                record["variant"],
+                record["expected_criteria"].split(";"),
+                record["comment"],
+            )
         )
 print(f"Number of variants: {len(variants)}")
 # ========================================

src/bench/comparison_v3.py

@@ -58,7 +58,11 @@
         if record["variant"].startswith("#"):
             continue
         variants.append(
-            (record["variant"], record["expected_criteria"].split(";"), record["comment"])
+            (
+                record["variant"],
+                record["expected_criteria"].split(";"),
+                record["comment"],
+            )
         )
 print(f"Number of variants: {len(variants)}")
 # ========================================

src/bench/comparison_v4.py

@@ -59,7 +59,11 @@
         if record["variant"].startswith("#"):
             continue
         variants.append(
-            (record["variant"], record["expected_criteria"].split(";"), record["comment"])
+            (
+                record["variant"],
+                record["expected_criteria"].split(";"),
+                record["comment"],
+            )
         )
 print(f"Number of variants: {len(variants)}")
 # ========================================
@@ -154,7 +158,7 @@ def eval_autoacmg(pred: Optional[AutoACMGSeqVarResult], expected: List[str]):
         return [], [], expected, []
     crit_met: List[str] = []
     for crit in pred.criteria:
-        if crit[1].prediction == AutoACMGPrediction.Met:
+        if crit[1].prediction == AutoACMGPrediction.Applicable:
             crit_met.append(crit[1].name)
     tp = list(set(expected) & set(crit_met))
     fn = list(set(expected) - set(crit_met))

src/bench/genebe.py

@@ -26,17 +26,26 @@
         if record["variant"].startswith("#"):
             continue
         variants.append(
-            (record["variant"], record["expected_criteria"].split(";"), record["comment"])
+            (
+                record["variant"],
+                record["expected_criteria"].split(";"),
+                record["comment"],
+            )
         )
 print(f"Number of variants: {len(variants)}")
 # ========================================
 
 # =========== Run the benchmark ===========
 list_of_variants = gnb.parse_hgvs(
-    [variant[0] for variant in variants], username=genebe_username, api_key=genebe_api_key
+    [variant[0] for variant in variants],
+    username=genebe_username,
+    api_key=genebe_api_key,
 )
 df = gnb.annotate_variants_list_to_dataframe(
-    list_of_variants, flatten_consequences=True, username=genebe_username, api_key=genebe_api_key
+    list_of_variants,
+    flatten_consequences=True,
+    username=genebe_username,
+    api_key=genebe_api_key,
 )
 
 # Export the dataframe to a csv file

src/bench/preprocess_data.ipynb

@@ -20,7 +20,6 @@
    ],
    "source": [
     "import os\n",
-    "import sys\n",
     "import pandas as pd\n",
     "from src.core.config import settings"
    ]
@@ -36,7 +35,7 @@
     "file_path = os.path.join(path_to_root, \"src\", \"bench\", \"clingen.txt\")\n",
     "\n",
     "# Load the data into a pandas DataFrame\n",
-    "data = pd.read_csv(file_path, sep='\\t')\n",
+    "data = pd.read_csv(file_path, sep=\"\\t\")\n",
     "\n",
     "# Display the first few rows of the DataFrame to understand its structure\n",
     "data.head()"
@@ -49,20 +48,19 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "\n",
     "# Extract the required fields: Variant name, Mode of Inheritance, and add Guideline to Comment\n",
-    "data['Variant'] = data['Variation']\n",
-    "data['Mode of Inheritance'] = data['Mode of Inheritance']\n",
-    "data['Comment'] = data['Guideline']\n",
+    "data[\"Variant\"] = data[\"Variation\"]\n",
+    "data[\"Mode of Inheritance\"] = data[\"Mode of Inheritance\"]\n",
+    "data[\"Comment\"] = data[\"Guideline\"]\n",
     "\n",
     "# Select only the required columns\n",
-    "result = data[['Variant', 'Mode of Inheritance', 'Comment']]\n",
+    "result = data[[\"Variant\", \"Mode of Inheritance\", \"Comment\"]]\n",
     "\n",
     "# Display the processed DataFrame\n",
     "result.head()\n",
     "\n",
     "# Save the result to a new CSV file\n",
-    "output_file_path = '/path/to/your/outputfile.csv'\n",
+    "output_file_path = \"/path/to/your/outputfile.csv\"\n",
     "result.to_csv(output_file_path, index=False)\n",
     "\n",
     "# Print a message to indicate the process is complete\n",