Rename AutoBA1BS1BS2PM2 to AutoPM2BA1bS1BS2

src/criteria/auto_criteria.py

@@ -4,9 +4,9 @@
 
 from src.api.annonars import AnnonarsClient
 from src.core.config import Config
-from src.criteria.auto_ba1_bs1_bs2_pm2 import AutoBA1BS1BS2PM2
 from src.criteria.auto_bp7 import AutoBP7
 from src.criteria.auto_pm1 import AutoPM1
+from src.criteria.auto_pm2_ba1_bs1_bs2 import AutoPM2BA1BS1BS2
 from src.criteria.auto_pm4_bp3 import AutoPM4BP3
 from src.criteria.auto_pp2_bp1 import AutoPP2BP1
 from src.criteria.auto_pp3_bp4 import AutoPP3BP4
@@ -100,7 +100,7 @@ def predict(self) -> Optional[ACMGResult]:
         # BA1, BS1, BS2, PM2
         try:
             logger.info("Predicting BA1, BS1, BS2, and PM2 criteria.")
-            ba1bs1bs2pm2 = AutoBA1BS1BS2PM2(self.seqvar, variant_info.result, config=self.config)
+            ba1bs1bs2pm2 = AutoPM2BA1BS1BS2(self.seqvar, variant_info.result, config=self.config)
             ba1bs1bs2pm2_prediction, ba1bs1bs2pm2_comment = ba1bs1bs2pm2.predict()
             if not ba1bs1bs2pm2_prediction:
                 logger.error("Failed to predict BA1, BS1, BS2, and PM2 criteria.")

src/criteria/auto_ba1_bs1_bs2_pm2.py → src/criteria/auto_pm2_ba1_bs1_bs2.py

@@ -15,8 +15,8 @@
 from src.utils import SeqVarTranscriptsHelper
 
 
-class AutoBA1BS1BS2PM2:
-    """Predicts BA1, BS1, BS2, PM2 criteria for sequence variants."""
+class AutoPM2BA1BS1BS2:
+    """Predicts PM2, BA1, BS1, BS2 criteria for sequence variants."""
 
     def __init__(
         self,
@@ -271,10 +271,12 @@ def _check_zyg(self, seqvar: SeqVar, variant_data: VariantResult) -> bool:
 
     def predict(self) -> Tuple[Optional[BA1BS1BS2PM2], str]:
         """
-        Predicts the BA1, BS1, BS2, PM2 criteria for the sequence variant.
+        Predicts the PM2, BA1, BS1, BS2 criteria for the sequence variant.
 
         Note:
             Rules:
+            PM2: Absent from controls allele frequency data.
+
             BA1: Allele frequency is >5%.
 
             BS1: Allele frequency is between 1% and 5%.
@@ -283,8 +285,6 @@ def predict(self) -> Tuple[Optional[BA1BS1BS2PM2], str]:
             (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an
             early age.
 
-            PM2: Absent from controls allele frequency data.
-
         Returns:
             BA1BS1BS2PM2: The prediction result.
         """
@@ -311,8 +311,8 @@ def predict(self) -> Tuple[Optional[BA1BS1BS2PM2], str]:
                 self.prediction.BS2 = True
 
         except AutoAcmgBaseException as e:
-            logger.error("Error occurred during BA1, BS1, BS2, PM2 prediction. Error: {}", e)
-            self.comment += f"An error occurred while predicting BA1, BS1, BS2, PM2 criteria: {e}"
+            logger.error("Error occurred during PM2, BA1, BS1, BS2 prediction. Error: {}", e)
+            self.comment += f"An error occurred while predicting PM2, BA1, BS1, BS2 criteria: {e}"
             self.prediction = None
 
         # Return the prediction result and explanation

tests/integ/test_integ_ba1_bs1_bs2_pm2.py → tests/integ/test_integ_pm2_ba1_bs1_bs2.py

@@ -1,13 +1,13 @@
-"""Integration tests for `BA1`, `BS1`, `BS2`, `PM2` criteria using upstream server."""
+"""Integration tests for `PM2`, `BA1`, `BS1`, `BS2` criteria using upstream server."""
 
 from typing import Tuple
 
 import pytest
 
 from src.auto_acmg import AutoACMG
 from src.core.config import Config
-from src.criteria.auto_ba1_bs1_bs2_pm2 import AutoBA1BS1BS2PM2
 from src.criteria.auto_criteria import AutoACMGCriteria
+from src.criteria.auto_pm2_ba1_bs1_bs2 import AutoPM2BA1BS1BS2
 from src.defs.annonars_variant import AnnonarsVariantResponse
 from src.defs.genome_builds import GenomeRelease
 from src.defs.seqvar import SeqVar
@@ -23,9 +23,9 @@
         # ("NM_000277.2(PAH):c.707-7A>T", GenomeRelease.GRCh37, [True, False, False, False]),
         # ("NM_000277.2(PAH):c.1242C>T", GenomeRelease.GRCh37, [False, True, True, False]),
         # ("NM_000277.2(PAH):c.1A>G", GenomeRelease.GRCh37, [False, False, False, True]),
-        ("NM_000277.2(PAH):c.503delA", GenomeRelease.GRCh37, [False, False, False, True]),
-        ("NM_000277.1(PAH):c.814G>T", GenomeRelease.GRCh37, [False, False, False, True]),
-        ("NM_000277.1(PAH):c.1162G>A", GenomeRelease.GRCh37, [False, False, False, True]),
+        ("NM_000277.2(PAH):c.503delA", GenomeRelease.GRCh37, [True, False, False, False]),
+        ("NM_000277.1(PAH):c.814G>T", GenomeRelease.GRCh37, [True, False, False, False]),
+        ("NM_000277.1(PAH):c.1162G>A", GenomeRelease.GRCh37, [True, False, False, False]),
         # ("NM_000277.1(PAH):c.722G>A", GenomeRelease.GRCh37, [False, False, False, True]),
         # ("NM_000277.2(PAH):c.735G>A", GenomeRelease.GRCh37, (True, False, True, False)),
         # ("NM_000314.6(PTEN):c.-1311T>C", GenomeRelease.GRCh37, (True, False, False, False)),
@@ -70,7 +70,7 @@
         # ("NM_000277.2(PAH):c.504C>A", GenomeRelease.GRCh37, (False, False, False, True)),
     ],
 )
-def test_ba1_bs1_bs2_pm2(
+def test_pm2_ba1_bs1_bs2(
     variant_name: str,
     genome_release: GenomeRelease,
     expected_prediction: Tuple[bool, bool, bool, bool],
@@ -84,15 +84,15 @@ def test_ba1_bs1_bs2_pm2(
     auto_acmg_criteria = AutoACMGCriteria(seqvar, config=config)
     variant_info = auto_acmg_criteria._get_variant_info(seqvar)
     assert isinstance(variant_info, AnnonarsVariantResponse)
-    # Then, predict BA1, BS1, BS2, PM2
-    auto_ba1_bs1_bs2_pm2 = AutoBA1BS1BS2PM2(seqvar, variant_info.result, config=config)
-    prediction, details = auto_ba1_bs1_bs2_pm2.predict()
+    # Then, predict PM2, BA1, BS1, BS2
+    auto_pm2_ba1_bs1_bs2 = AutoPM2BA1BS1BS2(seqvar, variant_info.result, config=config)
+    prediction, details = auto_pm2_ba1_bs1_bs2.predict()
     print(details)
     if expected_prediction is None:
         assert prediction is None, f"Failed for {variant_name}"
     else:
         assert prediction
-        assert prediction.BA1 == expected_prediction[0], f"Failed for {variant_name}"
-        assert prediction.BS1 == expected_prediction[1], f"Failed for {variant_name}"
-        assert prediction.BS2 == expected_prediction[2], f"Failed for {variant_name}"
-        assert prediction.PM2 == expected_prediction[3], f"Failed for {variant_name}"
+        assert prediction.PM2 == expected_prediction[0], f"Failed for {variant_name}"
+        assert prediction.BA1 == expected_prediction[1], f"Failed for {variant_name}"
+        assert prediction.BS1 == expected_prediction[2], f"Failed for {variant_name}"
+        assert prediction.BS2 == expected_prediction[3], f"Failed for {variant_name}"