Reimplement AutoPS1PM5 (#130)

* update dependencies

* add integration tests

* integration tests

* add integration tests for PS1 PM5

* wip

* add tests

* rename assets

* add missense check for PS1/PM5

* minor

src/api/annonars.py

@@ -1,5 +1,6 @@
 """Annonars API client."""
 
+from time import sleep
 from typing import Any, Optional
 
 import requests

src/auto_acmg.py

@@ -149,7 +149,7 @@ def predict(self) -> Optional[AutoACMGResult]:
             # PVS1
             try:
                 logger.info("Predicting PVS1.")
-                pvs1 = AutoPVS1(self.seqvar, self.genome_release, config=self.config)
+                pvs1 = AutoPVS1(self.seqvar, config=self.config)
                 seqvar_prediction, seqvar_prediction_path, comment = pvs1.predict()
                 if seqvar_prediction is None or seqvar_prediction_path is None:
                     raise AutoAcmgBaseException(
@@ -182,9 +182,7 @@ def predict(self) -> Optional[AutoACMGResult]:
             # Other criteria
             try:
                 logger.info("Predicting other ACMG criteria.")
-                auto_criteria = AutoACMGCriteria(
-                    self.seqvar, self.genome_release, config=self.config
-                )
+                auto_criteria = AutoACMGCriteria(self.seqvar, config=self.config)
                 criteria_preciction = auto_criteria.predict()
                 if criteria_preciction is None:
                     raise AutoAcmgBaseException("Other ACMG criteria prediction failed.")

src/criteria/auto_ba1_bs1_bs2_pm2.py

@@ -20,23 +20,22 @@ class AutoBA1BS1BS2PM2:
     def __init__(
         self,
         seqvar: SeqVar,
-        genome_release: GenomeRelease,
         variant_info: VariantResult,
         *,
         config: Optional[Config] = None,
     ):
         #: Configuration to use.
-        self.config = config or Config()
+        self.config: Config = config or Config()
         #: Sequence variant to predict.
-        self.seqvar = seqvar
-        #: Genome release.
-        self.genome_release = genome_release
+        self.seqvar: SeqVar = seqvar
         #: Variant information.
-        self.variant_info = variant_info
+        self.variant_info: VariantResult = variant_info
         #: Annonars client.
-        self.annonars_client = AnnonarsClient(api_base_url=self.config.api_base_url_annonars)
+        self.annonars_client: AnnonarsClient = AnnonarsClient(
+            api_base_url=self.config.api_base_url_annonars
+        )
         #: Prediction result.
-        self.prediction: BA1BS1BS2PM2 | None = None
+        self.prediction: Optional[BA1BS1BS2PM2] = None
         #: Comment to store the prediction explanation.
         self.comment: str = ""
 

src/criteria/auto_bp7.py

@@ -21,23 +21,22 @@ class AutoBP7:
     def __init__(
         self,
         seqvar: SeqVar,
-        genome_release: GenomeRelease,
         variant_info: VariantResult,
         *,
-        config: Config,
+        config: Optional[Config] = None,
     ):
         #: Configuration to use.
-        self.config = config or Config()
+        self.config: Config = config or Config()
         #: Sequence variant to predict.
-        self.seqvar = seqvar
-        #: Genome release.
-        self.genome_release = genome_release
+        self.seqvar: SeqVar = seqvar
         #: Variant information.
-        self.variant_info = variant_info
+        self.variant_info: VariantResult = variant_info
         #: Annonars client.
-        self.annonars_client = AnnonarsClient(api_base_url=config.api_base_url_annonars)
+        self.annonars_client: AnnonarsClient = AnnonarsClient(
+            api_base_url=self.config.api_base_url_annonars
+        )
         #: Prediction result.
-        self.prediction: BP7 | None = None
+        self.prediction: Optional[BP7] = None
         #: Comment to store the prediction explanation.
         self.comment: str = ""
 

src/criteria/auto_criteria.py

@@ -21,15 +21,14 @@
 class AutoACMGCriteria:
     """Predict ACMG criteria for sequence variant."""
 
-    def __init__(
-        self, seqvar: SeqVar, genome_release: GenomeRelease, *, config: Optional[Config] = None
-    ):
+    def __init__(self, seqvar: SeqVar, *, config: Optional[Config] = None):
         #: Configuration to use.
-        self.config = config or Config()
+        self.config: Config = config or Config()
         # Attributes to be set
-        self.seqvar = seqvar
-        self.genome_release = genome_release
-        self.annonars_client = AnnonarsClient(api_base_url=self.config.api_base_url_annonars)
+        self.seqvar: SeqVar = seqvar
+        self.annonars_client: AnnonarsClient = AnnonarsClient(
+            api_base_url=self.config.api_base_url_annonars
+        )
         self.prediction: Optional[ACMGResult] = None
 
     def _get_variant_info(self, seqvar: SeqVar) -> Optional[AnnonarsVariantResponse]:
@@ -57,9 +56,7 @@ def predict(self) -> Optional[ACMGResult]:
         # PS1 and PM5
         try:
             logger.info("Predicting PS1 and PM5 criteria.")
-            ps1pm5 = AutoPS1PM5(
-                self.seqvar, self.genome_release, variant_info.result, config=self.config
-            )
+            ps1pm5 = AutoPS1PM5(self.seqvar, variant_info.result, config=self.config)
             ps1_pm5_prediction, ps1_pm5_comment = ps1pm5.predict()
             if not ps1_pm5_prediction:
                 logger.error("Failed to predict PS1&PM5 criteria.")
@@ -81,9 +78,7 @@ def predict(self) -> Optional[ACMGResult]:
         # PM4 and BP3
         try:
             logger.info("Predicting PM4 and BP3 criteria.")
-            pm4bp3 = AutoPM4BP3(
-                self.seqvar, self.genome_release, variant_info.result, config=self.config
-            )
+            pm4bp3 = AutoPM4BP3(self.seqvar, variant_info.result, config=self.config)
             pm4_bp3_prediction, pm4_bp3_comment = pm4bp3.predict()
             if not pm4_bp3_prediction:
                 logger.error("Failed to predict PM4&BP3 criteria.")
@@ -105,9 +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, self.genome_release, variant_info.result, config=self.config
-            )
+            ba1bs1bs2pm2 = AutoBA1BS1BS2PM2(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.")
@@ -147,7 +140,7 @@ def predict(self) -> Optional[ACMGResult]:
         # PM1
         try:
             logger.info("Predicting PM1 criteria.")
-            pm1 = AutoPM1(self.seqvar, self.genome_release, variant_info.result, config=self.config)
+            pm1 = AutoPM1(self.seqvar, variant_info.result, config=self.config)
             pm1_prediction, pm1_comment = pm1.predict()
             if not pm1_prediction:
                 logger.error("Failed to predict PM1 criteria.")
@@ -164,9 +157,7 @@ def predict(self) -> Optional[ACMGResult]:
         # PP2 and BP1
         try:
             logger.info("Predicting PP2 and BP1 criteria.")
-            pp2bp1 = AutoPP2BP1(
-                self.seqvar, self.genome_release, variant_info.result, config=self.config
-            )
+            pp2bp1 = AutoPP2BP1(self.seqvar, variant_info.result, config=self.config)
             pp2_bp1_prediction, pp2_bp1_comment = pp2bp1.predict()
             if not pp2_bp1_prediction:
                 logger.error("Failed to predict PP2 and BP1 criteria.")
@@ -187,7 +178,7 @@ def predict(self) -> Optional[ACMGResult]:
         # BP7
         try:
             logger.info("Predicting BP7 criteria.")
-            bp7 = AutoBP7(self.seqvar, self.genome_release, variant_info.result, config=self.config)
+            bp7 = AutoBP7(self.seqvar, variant_info.result, config=self.config)
             bp7_prediction, bp7_comment = bp7.predict()
             if not bp7_prediction:
                 logger.error("Failed to predict BP7 criteria.")
@@ -204,9 +195,7 @@ def predict(self) -> Optional[ACMGResult]:
         # PP3 and BP4
         try:
             logger.info("Predicting PP3 and BP4 criteria.")
-            pp3_bp4 = AutoPP3BP4(
-                self.seqvar, self.genome_release, variant_info.result, config=self.config
-            )
+            pp3_bp4 = AutoPP3BP4(self.seqvar, variant_info.result, config=self.config)
             pp3_bp4_prediction, pp3_bp4_comment = pp3_bp4.predict()
             if not pp3_bp4_prediction:
                 logger.error("Failed to predict PP3 and BP4 criteria.")

src/criteria/auto_pm1.py

@@ -19,23 +19,22 @@ class AutoPM1:
     def __init__(
         self,
         seqvar: SeqVar,
-        genome_release: GenomeRelease,
         variant_info: VariantResult,
         *,
-        config: Config,
+        config: Optional[Config] = None,
     ):
         #: Configuration to use.
-        self.config = config or Config()
+        self.config: Config = config or Config()
         #: Sequence variant to predict.
-        self.seqvar = seqvar
-        #: Genome release.
-        self.genome_release = genome_release
+        self.seqvar: SeqVar = seqvar
         #: Variant information.
-        self.variant_info = variant_info
+        self.variant_info: VariantResult = variant_info
         #: Annonars client.
-        self.annonars_client = AnnonarsClient(api_base_url=config.api_base_url_annonars)
+        self.annonars_client: AnnonarsClient = AnnonarsClient(
+            api_base_url=self.config.api_base_url_annonars
+        )
         #: Prediction result.
-        self.prediction: PM1 | None = None
+        self.prediction: Optional[PM1] = None
         #: Comment to store the prediction explanation.
         self.comment: str = ""
 

src/criteria/auto_pm4_bp3.py

@@ -19,23 +19,22 @@ class AutoPM4BP3:
     def __init__(
         self,
         seqvar: SeqVar,
-        genome_release: GenomeRelease,
         variant_info: VariantResult,
         *,
         config: Optional[Config] = None,
     ):
         #: Configuration to use.
-        self.config = config or Config()
+        self.config: Config = config or Config()
         #: Sequence variant to predict.
-        self.seqvar = seqvar
-        #: Genome release.
-        self.genome_release = genome_release
+        self.seqvar: SeqVar = seqvar
         #: Variant information.
-        self.variant_info = variant_info
+        self.variant_info: VariantResult = variant_info
         #: Annonars client.
-        self.annonars_client = AnnonarsClient(api_base_url=self.config.api_base_url_annonars)
+        self.annonars_client: AnnonarsClient = AnnonarsClient(
+            api_base_url=self.config.api_base_url_annonars
+        )
         #: Prediction result.
-        self.prediction: PM4BP3 | None = None
+        self.prediction: Optional[PM4BP3] = None
         #: Comment to store the prediction explanation.
         self.comment: str = ""
 

src/criteria/auto_pp2_bp1.py

@@ -28,23 +28,22 @@ class AutoPP2BP1:
     def __init__(
         self,
         seqvar: SeqVar,
-        genome_release: GenomeRelease,
         variant_info: VariantResult,
         *,
-        config: Config,
+        config: Optional[Config] = None,
     ):
         #: Configuration to use.
-        self.config = config or Config()
+        self.config: Config = config or Config()
         #: Sequence variant to predict.
-        self.seqvar = seqvar
-        #: Genome release.
-        self.genome_release = genome_release
+        self.seqvar: SeqVar = seqvar
         #: Variant information.
-        self.variant_info = variant_info
+        self.variant_info: VariantResult = variant_info
         #: Annonars client.
-        self.annonars_client = AnnonarsClient(api_base_url=config.api_base_url_annonars)
+        self.annonars_client: AnnonarsClient = AnnonarsClient(
+            api_base_url=self.config.api_base_url_annonars
+        )
         #: Prediction result.
-        self.prediction: PP2BP1 | None = None
+        self.prediction: Optional[PP2BP1] = None
         #: Comment to store the prediction explanation.
         self.comment: str = ""
 

src/criteria/auto_pp3_bp4.py

@@ -19,23 +19,22 @@ class AutoPP3BP4:
     def __init__(
         self,
         seqvar: SeqVar,
-        genome_release: GenomeRelease,
         variant_info: VariantResult,
         *,
-        config: Config,
+        config: Optional[Config] = None,
     ):
         #: Configuration to use.
-        self.config = config or Config()
+        self.config: Config = config or Config()
         #: Sequence variant to predict.
-        self.seqvar = seqvar
-        #: Genome release.
-        self.genome_release = genome_release
+        self.seqvar: SeqVar = seqvar
         #: Variant information.
-        self.variant_info = variant_info
+        self.variant_info: VariantResult = variant_info
         #: Annonars client.
-        self.annonars_client = AnnonarsClient(api_base_url=config.api_base_url_annonars)
+        self.annonars_client: AnnonarsClient = AnnonarsClient(
+            api_base_url=self.config.api_base_url_annonars
+        )
         #: Prediction result.
-        self.prediction: PP3BP4 | None = None
+        self.prediction: Optional[PP3BP4] = None
         #: Comment to store the prediction explanation.
         self.comment: str = ""