Merge pull request #88 from cancervariants/issue-87

Fix label in variation descriptor
cancervariants · Apr 13, 2021 · 18fb631 · 18fb631
2 parents e44197a + 7962a34
commit 18fb631
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/tests/test_normalize.py b/tests/test_normalize.py
@@ -49,7 +49,7 @@ def braf_v600e():
             },
             "type": "Allele"
         },
-        "label": "NP_001361187.1%3Ap.Val640Glu",
+        "label": "NP_001361187.1:p.Val640Glu",
         "molecule_context": "protein",
         "structural_type": "SO:0001606",
         "ref_allele_seq": "V",
@@ -138,7 +138,7 @@ def vhl():
             },
             "type": "Allele"
         },
-        "label": "NP_000542.1%3Ap.Tyr185Ter",
+        "label": "NP_000542.1:p.Tyr185Ter",
         "molecule_context": "protein",
         "structural_type": "SO:0001606",
         "ref_allele_seq": "Y",
@@ -209,7 +209,7 @@ def vhl_silent():
     params = {
         "id": "normalize.variant:NP_000542.1%3Ap.Pro61%3D",
         "type": "VariationDescriptor",
-        "label": "NP_000542.1%3Ap.Pro61%3D",
+        "label": "NP_000542.1:p.Pro61=",
         "value_id": "ga4gh:VA.LBNTm7QqFZp1alJHaFKlKuRY9cOfdHeI",
         "value": {
             "location": {

diff --git a/variant/__init__.py b/variant/__init__.py
@@ -4,7 +4,7 @@
 import logging
 from ftplib import FTP
 
-__version__ = "0.1.11"
+__version__ = "0.1.12"
 
 APP_ROOT = Path(__file__).resolve().parents[0]
 

diff --git a/variant/normalize.py b/variant/normalize.py
@@ -33,14 +33,14 @@ def normalize(self, q, validations, amino_acid_cache):
             for r in validations.valid_results:
                 if r.mane_transcript:
                     valid_result = r
-                    label = quote(valid_result.mane_transcript.strip())
+                    label = valid_result.mane_transcript.strip()
                     break
             if not valid_result:
                 warning = f"Unable to find MANE Select Transcript for {q}."
                 logger.warning(warning)
                 warnings.append(warning)
                 valid_result = validations.valid_results[0]
-                label = quote(' '.join(q.strip().split()))
+                label = ' '.join(q.strip().split())
 
             valid_result_tokens = valid_result.classification.all_tokens