diff --git a/tests/test_normalize.py b/tests/test_normalize.py index 9d419298..d7973ffe 100644 --- 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 index d9f3cfaa..6b7eaf3b 100644 --- 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 index e07fcff8..c6fb13eb 100644 --- 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