Merge pull request #82 from monarch-initiative/to_string

#81
monarch-initiative · Oct 19, 2023 · 7e891cb · 7e891cb
2 parents 4b7a714 + fdbcab4
commit 7e891cb
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Showing 3 changed files with 8 additions and 134 deletions.
diff --git a/notebooks/STXBP1/input/PMID_35190816_STX_23708187_T23289.json b/notebooks/STXBP1/input/PMID_35190816_STX_23708187_T23289.json
diff --git a/src/genophenocorr/model/_variant.py b/src/genophenocorr/model/_variant.py
@@ -307,25 +307,22 @@ def __len__(self):
 
     def __eq__(self, other) -> bool:
         return isinstance(other, VariantCoordinates) \
-            and self.alt == other.alt \
+            and self.region == other.region \
             and self.ref == other.ref \
-            and self.chrom == other.chrom \
-            and self.start == other.start \
-            and self.end == other.end \
+            and self.alt == other.alt \
             and self.change_length == other.change_length
 
+    def __hash__(self) -> int:
+        return hash((self._region, self._ref, self._alt, self._change_length))
+
     def __str__(self) -> str:
-        return f"VariantCoordinates(chrom={self.chrom}, " \
-               f"start={self.start}, end={self.end}, " \
+        return f"VariantCoordinates(region={self.region}, " \
                f"ref={self.ref}, alt={self.alt}, " \
                f"change_length={self.change_length})"
 
     def __repr__(self) -> str:
         return str(self)
 
-    def __hash__(self) -> int:
-        return hash((self._region, self._ref, self._alt, self._change_length))
-
 
 class VariantCoordinateAware(metaclass=abc.ABCMeta):
 

diff --git a/src/genophenocorr/preprocessing/_vep.py b/src/genophenocorr/preprocessing/_vep.py
@@ -118,11 +118,11 @@ def _process_item(self, item) -> typing.Optional[TranscriptAnnotation]:
                                     protein_effect_start,
                                     protein_effect_end)
 
-    def _query_vep(self, variant_coordinates) -> dict:
+    def _query_vep(self, variant_coordinates: VariantCoordinates) -> dict:
         api_url = self._url % (verify_start_end_coordinates(variant_coordinates))
         r = requests.get(api_url, headers={'Content-Type': 'application/json'})
         if not r.ok:
-            self._logging.error(f"Expected a result but got an Error for variant: {variant_coordinates.as_string()}")
+            self._logging.error(f"Expected a result but got an Error for variant: {variant_coordinates}")
             r.raise_for_status()
         results = r.json()
         if not isinstance(results, list):