variation-normalizer 0.7.dev0__tar.gz → 0.7.0.dev5__tar.gz

{variation-normalizer-0.7.dev0/variation_normalizer.egg-info → variation-normalizer-0.7.0.dev5}/PKG-INFO

@@ -1,11 +1,12 @@
 Metadata-Version: 2.1
 Name: variation-normalizer
-Version: 0.7.dev0
+Version: 0.7.0.dev5
 Summary: VICC normalization routine for variations
 Home-page: https://github.com/cancervariants/variation-normalization
 Author: VICC
 Author-email: help@cancervariants.org
 License: MIT
+Platform: UNKNOWN
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
 Classifier: Intended Audience :: Developers
@@ -51,7 +52,7 @@ We are working towards adding more types of variations, coordinates, and represe
 
 The `/to_vrs` endpoint returns a list of validated VRS [Variations](https://vrs.ga4gh.org/en/1.2.0/terms_and_model.html#variation).
 
-The `/normalize` endpoint returns a [Variation Descriptor](https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/vod_index.html#variation-descriptor) containing the MANE Transcript, if one is found. If a genomic query is not given a gene, `normalize` will return its GRCh38 representation. Variation Normalizer relies on [UTA Tools](https://github.com/GenomicMedLab/uta-tools) for retrieving MANE Transcript data. More information on the transcript selection algorithm can be found [here](https://github.com/GenomicMedLab/uta-tools/blob/main/docs/TranscriptSelectionPriority.md).
+The `/normalize` endpoint returns a [Variation Descriptor](https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/vod_index.html#variation-descriptor) containing the MANE Transcript, if one is found. If a genomic query is not given a gene, `normalize` will return its GRCh38 representation. Variation Normalizer relies on [**C**ommon **O**perations **O**n **L**ots-of **Seq**uences Tool (cool-seq-tool)](https://github.com/GenomicMedLab/cool-seq-tool) for retrieving MANE Transcript data. More information on the transcript selection algorithm can be found [here](https://github.com/GenomicMedLab/cool-seq-tool/blob/main/docs/TranscriptSelectionPriority.md).
 
 ## Developer Instructions
 
@@ -110,8 +111,10 @@ sudo mv /usr/local/share/seqrepo/2021-01-29._fkuefgd /usr/local/share/seqrepo/20
 exit
 ```
 
+Use the `SEQREPO_ROOT_DIR` environment variable to set the path of an already existing SeqRepo directory. The default is `/usr/local/share/seqrepo/latest`.
+
 #### UTA
-Variation Normalizer also uses [UTA Tools](https://github.com/GenomicMedLab/uta-tools) which uses [UTA](https://github.com/biocommons/uta) as the underlying PostgreSQL database.
+Variation Normalizer also uses [**C**ommon **O**perations **O**n **L**ots-of **Seq**uences Tool (cool-seq-tool)](https://github.com/GenomicMedLab/cool-seq-tool) which uses [UTA](https://github.com/biocommons/uta) as the underlying PostgreSQL database.
 
 _The following commands will likely need modification appropriate for the installation environment._
 1. Install [PostgreSQL](https://www.postgresql.org/)
@@ -173,3 +176,5 @@ From the _root_ directory of the repository:
 ```
 pytest tests/
 ```
+
+

{variation-normalizer-0.7.dev0 → variation-normalizer-0.7.0.dev5}/README.md

@@ -31,7 +31,7 @@ We are working towards adding more types of variations, coordinates, and represe
 
 The `/to_vrs` endpoint returns a list of validated VRS [Variations](https://vrs.ga4gh.org/en/1.2.0/terms_and_model.html#variation).
 
-The `/normalize` endpoint returns a [Variation Descriptor](https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/vod_index.html#variation-descriptor) containing the MANE Transcript, if one is found. If a genomic query is not given a gene, `normalize` will return its GRCh38 representation. Variation Normalizer relies on [UTA Tools](https://github.com/GenomicMedLab/uta-tools) for retrieving MANE Transcript data. More information on the transcript selection algorithm can be found [here](https://github.com/GenomicMedLab/uta-tools/blob/main/docs/TranscriptSelectionPriority.md).
+The `/normalize` endpoint returns a [Variation Descriptor](https://vrsatile.readthedocs.io/en/latest/value_object_descriptor/vod_index.html#variation-descriptor) containing the MANE Transcript, if one is found. If a genomic query is not given a gene, `normalize` will return its GRCh38 representation. Variation Normalizer relies on [**C**ommon **O**perations **O**n **L**ots-of **Seq**uences Tool (cool-seq-tool)](https://github.com/GenomicMedLab/cool-seq-tool) for retrieving MANE Transcript data. More information on the transcript selection algorithm can be found [here](https://github.com/GenomicMedLab/cool-seq-tool/blob/main/docs/TranscriptSelectionPriority.md).
 
 ## Developer Instructions
 
@@ -90,8 +90,10 @@ sudo mv /usr/local/share/seqrepo/2021-01-29._fkuefgd /usr/local/share/seqrepo/20
 exit
 ```
 
+Use the `SEQREPO_ROOT_DIR` environment variable to set the path of an already existing SeqRepo directory. The default is `/usr/local/share/seqrepo/latest`.
+
 #### UTA
-Variation Normalizer also uses [UTA Tools](https://github.com/GenomicMedLab/uta-tools) which uses [UTA](https://github.com/biocommons/uta) as the underlying PostgreSQL database.
+Variation Normalizer also uses [**C**ommon **O**perations **O**n **L**ots-of **Seq**uences Tool (cool-seq-tool)](https://github.com/GenomicMedLab/cool-seq-tool) which uses [UTA](https://github.com/biocommons/uta) as the underlying PostgreSQL database.
 
 _The following commands will likely need modification appropriate for the installation environment._
 1. Install [PostgreSQL](https://www.postgresql.org/)

{variation-normalizer-0.7.dev0 → variation-normalizer-0.7.0.dev5}/setup.cfg

@@ -27,29 +27,33 @@ install_requires =
 	fastapi
 	uvicorn
 	pydantic
-	ga4gh.vrs[extras] >= 0.8.7dev0
-	gene-normalizer >= 0.2.3
+	ga4gh.vrs[extras] >= 0.9.0.dev0
+	gene-normalizer >= 0.2.8
 	pyliftover
 	boto3
-	ga4gh.vrsatile.pydantic >= 0.1.dev3
-	uta-tools >= 0.1.2
+	ga4gh.vrsatile.pydantic >= 0.1.0.dev7
+	cool-seq-tool >= 0.1.11
+	bioutils
 tests_require = 
 	pytest
 	pytest-cov
 	pyyaml
 	pytest-asyncio
 
-[options.package_data]
-variation = 
-	data/amino_acids.csv
-	data/transcript_mapping.tsv
-
 [options.extras_require]
 dev = 
 	pytest
 	pytest-cov
-	pyyaml
 	psycopg2-binary
+	pytest-asyncio
+	flake8
+	flake8-docstrings
+	flake8-quotes
+	flake8-annotations
+	flake8-import-order
+	pre-commit
+	jupyter
+	ipykernel
 
 [tool:pytest]
 addopts = --ignore setup.py --ignore=codebuild/ --doctest-modules --cov-report term-missing --cov .

{variation-normalizer-0.7.dev0 → variation-normalizer-0.7.0.dev5}/tests/classifiers/classifier_base.py

@@ -3,9 +3,8 @@ import yaml
 from gene.query import QueryHandler as GeneQueryHandler
 
 from variation.tokenizers import Tokenize
-from tests import PROJECT_ROOT
-from variation.tokenizers.caches import AminoAcidCache
 from variation.tokenizers import GeneSymbol
+from tests import PROJECT_ROOT
 
 
 class ClassifierBase:
@@ -20,8 +19,7 @@ class ClassifierBase:
             {"should_match": [], "should_not_match": []}
         )
         self.classifier = self.classifier_instance()
-        self.tokenizer = Tokenize(AminoAcidCache(),
-                                  GeneSymbol(GeneQueryHandler()))
+        self.tokenizer = Tokenize(GeneSymbol(GeneQueryHandler()))
 
     def classifier_instance(self):
         """Check that the classifier_instance method is implemented."""

{variation-normalizer-0.7.dev0 → variation-normalizer-0.7.0.dev5}/tests/conftest.py

@@ -68,6 +68,7 @@ def vhl_gene_context():
                     "vega:OTTHUMG00000128668",
                     "ccds:CCDS2598",
                     "ena.embl:L15409",
+                    "iuphar:3204",
                     "orphanet:120467",
                     "ccds:CCDS2597",
                     "uniprot:P40337"
@@ -1019,9 +1020,9 @@ def braf_amplification(braf_ncbi_seq_loc, braf_gene_context):
         "id": "normalize.variation:BRAF%20Amplification",
         "type": "VariationDescriptor",
         "variation": {
-            "id": "ga4gh:RCN.avsI73-9i6ykDIRB3eB89jeU1lhyBbYt",
+            "id": "ga4gh:RCN.tXX8oMzsJx3r9ZlqQlzk_K8Luz-bswdT",
             "location": braf_ncbi_seq_loc,
-            "relative_copy_class": "high-level gain",
+            "relative_copy_class": "EFO:0030072",
             "type": "RelativeCopyNumber"
         },
         "molecule_context": "genomic",
@@ -1038,9 +1039,9 @@ def prpf8_amplification(prpf8_ncbi_seq_loc, prpf8_gene_context):
         "id": "normalize.variation:PRPF8%20AMPLIFICATION",
         "type": "VariationDescriptor",
         "variation": {
-            "id": "ga4gh:RCN.w44H1MxQusrCBDxUoLr30E1iJBMGXF14",
+            "id": "ga4gh:RCN.DW0vRfIA0aI4AR0epEh_k-qrB2pdpZVw",
             "location": prpf8_ncbi_seq_loc,
-            "relative_copy_class": "high-level gain",
+            "relative_copy_class": "EFO:0030072",
             "type": "RelativeCopyNumber"
         },
         "molecule_context": "genomic",

{variation-normalizer-0.7.dev0 → variation-normalizer-0.7.0.dev5}/tests/test_codon_table.py

@@ -2,13 +2,12 @@
 import pytest
 
 from variation.data_sources.codon_table import CodonTable
-from variation.tokenizers.caches import AminoAcidCache
 
 
 @pytest.fixture(scope="module")
 def test_codon_table():
     """Build codon table test fixture."""
-    return CodonTable(AminoAcidCache())
+    return CodonTable()
 
 
 def test_get_codons(test_codon_table):

{variation-normalizer-0.7.dev0 → variation-normalizer-0.7.0.dev5}/tests/test_gnomad_vcf_to_protein.py

@@ -798,8 +798,9 @@ async def test_substitution(test_handler, braf_v600e, braf_v600l,
 @pytest.mark.asyncio
 async def test_silent_mutation(test_handler, vhl_silent):
     """Test that silent queries return correct response"""
-    resp = await test_handler.gnomad_vcf_to_protein("3-10183714-C-C")
-    assertion_checks(resp.variation_descriptor, vhl_silent, "3-10183714-C-C",
+    # https://www.ncbi.nlm.nih.gov/clinvar/variation/379039/?new_evidence=true
+    resp = await test_handler.gnomad_vcf_to_protein("3-10142030-C-C")
+    assertion_checks(resp.variation_descriptor, vhl_silent, "3-10142030-C-C",
                      ignore_id=True)
     assert resp.warnings == []
 
@@ -850,8 +851,11 @@ async def test_invalid(test_handler):
     assert resp.variation_descriptor.variation.type == "Text"
     assert resp.variation_descriptor.label == "7-140753336-T-G"
     assert set(resp.warnings) == {
-        "Unable to get transcripts given NC_000007.13 and 140753336",
         "Expected T but found A on NC_000007.14 at position 140753336",
+        "Unable to get MANE data for NM_004333.6 using NC_000007.13 at positions"
+        " 140753335 to 140753335",  # MANE Select
+        "Unable to get MANE data for NM_001374258.1 using NC_000007.13 at positions"
+        " 140753335 to 140753335"  # MANE Plus Clinical
     }
 
     resp = await test_handler.gnomad_vcf_to_protein("20-2-TC-TG",

{variation-normalizer-0.7.dev0 → variation-normalizer-0.7.0.dev5}/tests/test_hgvs_dup_del_mode.py

@@ -1,4 +1,6 @@
 """Module for testing HGVS Dup Del mode."""
+from copy import deepcopy
+
 import pytest
 from ga4gh.vrsatile.pydantic.vrsatile_models import VariationDescriptor
 
@@ -318,9 +320,9 @@ def genomic_dup1_vrc(genomic_dup1, genomic_dup1_seq_loc):
     """Create a test fixture for genomic dup relative CNV."""
     genomic_dup1["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": "ga4gh:RCN.qSnPCsf9ylOaecpSBjTkxWFqxmmyYWtL",
+        "id": "ga4gh:RCN.UBQCyZ7lHIJN6FoQHp3gURfJSWN31S09",
         "location": genomic_dup1_seq_loc,
-        "relative_copy_class": "high-level gain"
+        "relative_copy_class": "EFO:0030072"
     }
     return VariationDescriptor(**genomic_dup1)
 
@@ -585,9 +587,9 @@ def genomic_dup2_vrc(genomic_dup2, genomic_dup2_seq_loc):
     """Create a test fixture for genomic dup relative CNV."""
     genomic_dup2["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": "ga4gh:RCN.zizBAY460E_wbra9Y6oCxojd8YCbIfnx",
+        "id": "ga4gh:RCN.ClUoNekweei4SUxyjxeLnxagD6vKQ1w7",
         "location": genomic_dup2_seq_loc,
-        "relative_copy_class": "low-level gain"
+        "relative_copy_class": "EFO:0030070"
     }
     return VariationDescriptor(**genomic_dup2)
 
@@ -729,12 +731,11 @@ def genomic_dup3_vac(genomic_dup3, genomic_del3_dup3_loc):
 @pytest.fixture(scope="module")
 def genomic_dup3_vrc(genomic_dup3, genomic_del3_dup3_loc):
     """Create a test fixture for genomic dup relative cnv."""
-    _id = "ga4gh:RCN.4m1TD2538i7v4NQ_OeJ-pIEhlRpYZ3_y"
     genomic_dup3["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": _id,
+        "id": "ga4gh:RCN.pkRuYZTdIFaA_b9TPc7Czk56VNj1xGz3",
         "location": genomic_del3_dup3_loc,
-        "relative_copy_class": "low-level gain"
+        "relative_copy_class": "EFO:0030070"
     }
     return VariationDescriptor(**genomic_dup3)
 
@@ -784,12 +785,11 @@ def genomic_dup3_free_text_subject():
 @pytest.fixture(scope="module")
 def genomic_dup3_free_text_vrc(genomic_dup3_free_text, genomic_dup3_free_text_subject):
     """Create a test fixture for genomic dup relative cnv."""
-    _id = "ga4gh:RCN.ReWfNwAnchjIPJQEXM038T9M3OsOO7yK"
     genomic_dup3_free_text["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": _id,
+        "id": "ga4gh:RCN.roF4IsQUR-ZxU_c4KMw9WoDrRnhfA75O",
         "location": genomic_dup3_free_text_subject,
-        "relative_copy_class": "low-level gain"
+        "relative_copy_class": "EFO:0030070"
     }
     return VariationDescriptor(**genomic_dup3_free_text)
 
@@ -839,12 +839,11 @@ def genomic_dup4():
 @pytest.fixture(scope="module")
 def genomic_dup4_vrc(genomic_dup4, genoimc_dup4_loc):
     """Create a test fixture for genomic dup relative cnv."""
-    _id = "ga4gh:RCN.uSGvLYzpzivqDzhuKR44DHc5imZJSmoV"
     genomic_dup4["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": _id,
+        "id": "ga4gh:RCN.cFmUKSZQQ-CuOqG468ZyP_zF63WflwoF",
         "location": genoimc_dup4_loc,
-        "relative_copy_class": "low-level gain"
+        "relative_copy_class": "EFO:0030070"
     }
     return VariationDescriptor(**genomic_dup4)
 
@@ -907,12 +906,11 @@ def genomic_dup4_free_text_subject():
 @pytest.fixture(scope="module")
 def genomic_dup4_free_text_vrc(genomic_dup4_free_text, genomic_dup4_free_text_subject):
     """Create a test fixture for genomic dup relative cnv."""
-    _id = "ga4gh:RCN.Cf9r8JDpUC18VkkEv44jf8b8WMqUIRFu"
     genomic_dup4_free_text["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": _id,
+        "id": "ga4gh:RCN.LB5BaDj-GkVlpVAIG9kJSir1uO4DoZ6X",
         "location": genomic_dup4_free_text_subject,
-        "relative_copy_class": "low-level gain"
+        "relative_copy_class": "EFO:0030070"
     }
     return VariationDescriptor(**genomic_dup4_free_text)
 
@@ -972,12 +970,11 @@ def genomic_dup5_abs_cnv(params, genomic_dup5_loc):
 
 def genomic_dup5_rel_cnv(params, genomic_dup5_loc):
     """Create genomic dup4 relative cnv"""
-    _id = "ga4gh:RCN.tr_brFSOfykm3I3ufLQTS9pV8KKjqLhK"
     params["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": _id,
+        "id": "ga4gh:RCN.1sn-uR3OiG0SbGd-f2IkujiqjcUHzxo3",
         "location": genomic_dup5_loc,
-        "relative_copy_class": "low-level gain"
+        "relative_copy_class": "EFO:0030070"
     }
 
 
@@ -1070,12 +1067,11 @@ def genomic_dup6():
 
 def genomic_dup6_rel_cnv(params, genoimc_dup6_loc):
     """Create genomic dup6 relative cnv"""
-    _id = "ga4gh:RCN.c5Uq3TFDNpQSyDlbXb0BRonw9AYHHk0H"
     params["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": _id,
+        "id": "ga4gh:RCN.Mb9dPwnAm_KSrifZ0955Lse7Ubr5PaGG",
         "location": genoimc_dup6_loc,
-        "relative_copy_class": "low-level gain"
+        "relative_copy_class": "EFO:0030070"
     }
 
 
@@ -1205,9 +1201,9 @@ def genomic_del1_vrc(genomic_del1, genomic_del1_seq_loc):
     """Create a test fixture for genomic del relative CNV."""
     genomic_del1["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": "ga4gh:RCN.z7MU8QUSR_aeWG7MP161H4jwPGoyo1No",
+        "id": "ga4gh:RCN.89rlJ6oV422qg04Rhb25rhZJF46LUPqR",
         "location": genomic_del1_seq_loc,
-        "relative_copy_class": "copy neutral"
+        "relative_copy_class": "EFO:0030067"
     }
     return VariationDescriptor(**genomic_del1)
 
@@ -1361,9 +1357,9 @@ def genomic_del2_vrc(genomic_del2, genomic_del2_seq_loc):
     """Create a test fixture for genomic del relative CNV."""
     genomic_del2["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": "ga4gh:RCN._19twDngCtP3U-8ED2Kly2HM53I_7CV7",
+        "id": "ga4gh:RCN.Ai0Z31nuQtHGJ-0Vl8ARrblr0xiKW9d-",
         "location": genomic_del2_seq_loc,
-        "relative_copy_class": "complete loss"
+        "relative_copy_class": "EFO:0030069"
     }
     return VariationDescriptor(**genomic_del2)
 
@@ -1492,12 +1488,11 @@ def genomic_del3():
 @pytest.fixture(scope="module")
 def genomic_del3_vrc(genomic_del3, genomic_del3_dup3_loc):
     """Create a test fixture for genomic del relative cnv."""
-    _id = "ga4gh:RCN.dYerC8FSiqcexo8X1n3XUKpAckoAsfOK"
     genomic_del3["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": _id,
+        "id": "ga4gh:RCN.OPd0F6EMNNugGkKFBbl4f1We0WwtL9uI",
         "location": genomic_del3_dup3_loc,
-        "relative_copy_class": "partial loss"
+        "relative_copy_class": "EFO:0030067"
     }
     return VariationDescriptor(**genomic_del3)
 
@@ -1678,12 +1673,11 @@ def genomic_del3_free_text_subject():
 @pytest.fixture(scope="module")
 def genomic_del3_free_text_vrc(genomic_del3_free_text, genomic_del3_free_text_subject):
     """Create a test fixture for genomic del relative cnv."""
-    _id = "ga4gh:RCN.6c0tRlHyFYGSeDEmSyn0nrZJLQDkwVsG"
     genomic_del3_free_text["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": _id,
+        "id": "ga4gh:RCN.jHNFu709utJ1TkGwQkY1NxmYfRqzof5N",
         "location": genomic_del3_free_text_subject,
-        "relative_copy_class": "partial loss"
+        "relative_copy_class": "EFO:0030067"
     }
     return VariationDescriptor(**genomic_del3_free_text)
 
@@ -1733,12 +1727,11 @@ def genomic_del4():
 @pytest.fixture(scope="module")
 def genomic_del4_vrc(genomic_del4, genomic_del4_seq_loc):
     """Create a test fixture for genomic del relative cnv."""
-    _id = "ga4gh:RCN.BwZOFAfo5u8TcwbR3DMi8qbIImv96VQU"
     genomic_del4["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": _id,
+        "id": "ga4gh:RCN.euSDpT11wTt9o9lzlk16lc340OBX2_ij",
         "location": genomic_del4_seq_loc,
-        "relative_copy_class": "partial loss"
+        "relative_copy_class": "EFO:0030067"
     }
     return VariationDescriptor(**genomic_del4)
 
@@ -1904,12 +1897,11 @@ def genomic_del4_free_text_subject():
 @pytest.fixture(scope="module")
 def genomic_del4_free_text_vrc(genomic_del4_free_text, genomic_del4_free_text_subject):
     """Create a test fixture for genomic del relative cnv."""
-    _id = "ga4gh:RCN.XqfrZ9k9mwDO0cM9duK7ooOih0iR1H2Q"
     genomic_del4_free_text["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": _id,
+        "id": "ga4gh:RCN.fcVXdxFIjLmULNFOLewLKq9xPvNeVNDm",
         "location": genomic_del4_free_text_subject,
-        "relative_copy_class": "partial loss"
+        "relative_copy_class": "EFO:0030067"
     }
     return VariationDescriptor(**genomic_del4_free_text)
 
@@ -1949,7 +1941,7 @@ def genomic_uncertain_del_2():
         "id": "normalize.variation:NC_000002.12%3Ag.%28%3F_110104900%29_%28110207160_%3F%29del",  # noqa: E501
         "type": "VariationDescriptor",
         "variation": {
-            "id": "ga4gh:RCN.7EM-Wsg_7mmAE1LW8cmRI3QwKhJCA24a",
+            "id": "ga4gh:RCN.0saHzDrnktHex2tkYyPxQanKwjLUZQu6",
             "location": {
                 "id": "ga4gh:SL.gUeB872FGVaphqoSAfI0gz4KXJvpZKL_",
                 "sequence_id": "ga4gh:SQ.pnAqCRBrTsUoBghSD1yp_jXWSmlbdh4g",
@@ -1965,7 +1957,7 @@ def genomic_uncertain_del_2():
                 },
                 "type": "SequenceLocation"
             },
-            "relative_copy_class": "partial loss",
+            "relative_copy_class": "EFO:0030067",
             "type": "RelativeCopyNumber"
         },
         "molecule_context": "genomic",
@@ -1981,7 +1973,7 @@ def genomic_uncertain_del_y():
         "id": "normalize.variation:NC_000024.10%3Ag.%28%3F_14076802%29_%2857165209_%3F%29del",  # noqa: E501
         "type": "VariationDescriptor",
         "variation": {
-            "id": "ga4gh:RCN.2q7DKevv8nUh87Sl00Z7l50h047Ti2at",
+            "id": "ga4gh:RCN.7Nl4T845v9vuVS4PUB8HI4-tLPsEWU6e",
             "location": {
                 "id": "ga4gh:SL.ykRzA8IFueiCG7oznnN4teL2nXXBshHV",
                 "sequence_id": "ga4gh:SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5",
@@ -1997,7 +1989,7 @@ def genomic_uncertain_del_y():
                 },
                 "type": "SequenceLocation"
             },
-            "relative_copy_class": "partial loss",
+            "relative_copy_class": "EFO:0030067",
             "type": "RelativeCopyNumber"
         },
         "molecule_context": "genomic",
@@ -2033,12 +2025,11 @@ def genomic_del5_abs_cnv(params, genomic_del5_seq_loc):
 
 def genomic_del5_rel_cnv(params, genomic_del5_seq_loc):
     """Create genomic del5 relative cnv"""
-    _id = "ga4gh:RCN.9rG3a5u3JODwQGVrv1IgAjG6SZgdvraH"
     params["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": _id,
+        "id": "ga4gh:RCN.P0LWls1SeRF881B-uhomC8B4BHc6Fo2R",
         "location": genomic_del5_seq_loc,
-        "relative_copy_class": "partial loss"
+        "relative_copy_class": "EFO:0030067"
     }
 
 
@@ -2247,12 +2238,11 @@ def genomic_del6():
 
 def genomic_del6_rel_cnv(params, genomic_del6_seq_loc):
     """Create genomic del6 relative cnv"""
-    _id = "ga4gh:RCN.zsagK87b_RdK4_QZGMnbNl39LCuJUjAr"
     params["variation"] = {
         "type": "RelativeCopyNumber",
-        "id": _id,
+        "id": "ga4gh:RCN.gQwVlnomQRAffyySAQdj3PYxnEalHrXK",
         "location": genomic_del6_seq_loc,
-        "relative_copy_class": "partial loss"
+        "relative_copy_class": "EFO:0030067"
     }
 
 
@@ -2483,7 +2473,7 @@ async def test_genomic_dup1(test_handler, genomic_dup1_lse,
     assertion_checks(resp.variation_descriptor, genomic_dup1_vac, q)
 
     resp = await test_handler.normalize(q, "relative_cnv",
-                                        relative_copy_class="high-level gain")
+                                        relative_copy_class="EFO:0030072")
     assertion_checks(resp.variation_descriptor, genomic_dup1_vrc, q)
 
     resp = await test_handler.normalize(q, "repeated_seq_expr")
@@ -2503,7 +2493,7 @@ async def test_genomic_dup1(test_handler, genomic_dup1_lse,
     assertion_checks(resp.variation_descriptor, genomic_dup1_vac, q, ignore_id=True)
 
     resp = await test_handler.normalize(q, "relative_cnv",
-                                        relative_copy_class="high-level gain")
+                                        relative_copy_class="EFO:0030072")
     assertion_checks(resp.variation_descriptor, genomic_dup1_vrc, q, ignore_id=True)
 
     resp = await test_handler.normalize(q, "repeated_seq_expr")
@@ -2628,8 +2618,11 @@ async def test_genomic_dup3(test_handler, genomic_dup3_vrc, genomic_dup3_vac,
     assertion_checks(resp.variation_descriptor, genomic_dup3_vac, q)
 
     resp = await test_handler.normalize(q, "relative_cnv",
-                                        relative_copy_class="low-level gain")
-    assertion_checks(resp.variation_descriptor, genomic_dup3_vrc, q)
+                                        relative_copy_class="EFO:0030071")
+    test_var = deepcopy(genomic_dup3_vrc)
+    test_var.variation.relative_copy_class = "EFO:0030071"
+    test_var.variation.id = "ga4gh:RCN.lR7qHx5BeS4yJlaopO8JteBq1AO3Kv9m"
+    assertion_checks(resp.variation_descriptor, test_var, q)
 
     resp = await test_handler.normalize(q, "repeated_seq_expr",
                                         untranslatable_returns_text=True)
@@ -2941,7 +2934,7 @@ async def test_genomic_del1(test_handler, genomic_del1_lse, genomic_del1_vac,
     assertion_checks(resp.variation_descriptor, genomic_del1_vac, q)
 
     resp = await test_handler.normalize(q, "relative_cnv",
-                                        relative_copy_class="copy neutral")
+                                        relative_copy_class="EFO:0030067")
     assertion_checks(resp.variation_descriptor, genomic_del1_vrc, q)
 
     resp = await test_handler.normalize(q, "repeated_seq_expr")
@@ -2958,7 +2951,7 @@ async def test_genomic_del1(test_handler, genomic_del1_lse, genomic_del1_vac,
     assertion_checks(resp.variation_descriptor, genomic_del1_vac, q, ignore_id=True)
 
     resp = await test_handler.normalize(q, "relative_cnv",
-                                        relative_copy_class="copy neutral")
+                                        relative_copy_class="EFO:0030067")
     assertion_checks(resp.variation_descriptor, genomic_del1_vrc, q, ignore_id=True)
 
     resp = await test_handler.normalize(q, "repeated_seq_expr")
@@ -3026,7 +3019,7 @@ async def test_genomic_del2(test_handler, genomic_del2_lse, genomic_del2_vac,
     assertion_checks(resp.variation_descriptor, genomic_del2_vac, q)
 
     resp = await test_handler.normalize(q, "relative_cnv",
-                                        relative_copy_class="complete loss")
+                                        relative_copy_class="EFO:0030069")
     assertion_checks(resp.variation_descriptor, genomic_del2_vrc, q)
 
     resp = await test_handler.normalize(q, "repeated_seq_expr")
@@ -3043,7 +3036,7 @@ async def test_genomic_del2(test_handler, genomic_del2_lse, genomic_del2_vac,
     assertion_checks(resp.variation_descriptor, genomic_del2_vac, q, ignore_id=True)
 
     resp = await test_handler.normalize(q, "relative_cnv",
-                                        relative_copy_class="complete loss")
+                                        relative_copy_class="EFO:0030069")
     assertion_checks(resp.variation_descriptor, genomic_del2_vrc, q, ignore_id=True)
 
     resp = await test_handler.normalize(q, "repeated_seq_expr")

{variation-normalizer-0.7.dev0 → variation-normalizer-0.7.0.dev5}/tests/test_normalize.py

@@ -517,6 +517,36 @@ def coding_dna_deletion(erbb2_context):
     return VariationDescriptor(**params)
 
 
+@pytest.fixture(scope="module")
+def genomic_deletion():
+    """Create test fixture for genomic deletion range with deleted sequence.
+    (CA915940709)
+    """
+    params = {
+        "id": "normalize.variation:NC_000003.12%3Ag.10146527_10146528del",
+        "type": "VariationDescriptor",
+        "variation": {
+            "id": "ga4gh:VA.AoFRR6KWkw6_YfrGAxGkT9SJsXieSk93",
+            "location": {
+                "id": "ga4gh:SL.6D7Wbq7XOvga3y-057BKIra4g9RgAFy9",
+                "end": {"value": 10146528, "type": "Number"},
+                "start": {"value": 10146524, "type": "Number"},
+                "sequence_id": "ga4gh:SQ.Zu7h9AggXxhTaGVsy7h_EZSChSZGcmgX",
+                "type": "SequenceLocation"
+            },
+            "state": {
+                "sequence": "CT",
+                "type": "LiteralSequenceExpression"
+            },
+            "type": "Allele"
+        },
+        "molecule_context": "genomic",
+        "structural_type": "SO:0000159",
+        "vrs_ref_allele_seq": "CTCT"
+    }
+    return VariationDescriptor(**params)
+
+
 @pytest.fixture(scope="module")
 def coding_dna_insertion(limk2_gene_context):
     """Create test fixture for coding DNA insertion."""
@@ -1087,14 +1117,30 @@ async def test_protein_deletion(test_handler, protein_deletion_np_range):
     assertion_checks(resp.variation_descriptor, protein_deletion_np_range,
                      "ERBB2 Leu755_Thr759del")
 
+    resp1 = await test_handler.normalize("EGFR L747_T751del")
+    resp2 = await test_handler.normalize("EGFR L747_T751delLREAT")
+    assert resp1.variation_descriptor.variation.id == \
+        resp2.variation_descriptor.variation.id
+
+    # incorrect deleted sequence
+    resp = await test_handler.normalize("EGFR L747_T751delLREA")
+    assert not resp.variation_descriptor
+
 
 @pytest.mark.asyncio
 async def test_coding_dna_deletion(test_handler, coding_dna_deletion):
     """Test that coding dna deletion normalizes correctly."""
     # https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA645372623  # noqa: E501
     q = "NM_004448.3:c.2264_2278delTGAGGGAAAACACAT"
-    resp = await test_handler.normalize(q)
-    assertion_checks(resp.variation_descriptor, coding_dna_deletion, q)
+    resp1 = await test_handler.normalize(q)
+    assertion_checks(resp1.variation_descriptor, coding_dna_deletion, q)
+
+    # incorrected deleted sequence
+    resp = await test_handler.normalize("NM_004448.3:c.2264_2278delTGAGGGAAAACACTA")
+    assert not resp.variation_descriptor
+
+    resp2 = await test_handler.normalize("NM_004448.3:c.2264_2278del")
+    assert resp1.variation_descriptor.variation.id == resp2.variation_descriptor.variation.id  # noqa: E501
 
     q = "ERBB2 c.2264_2278delTGAGGGAAAACACAT"
     resp = await test_handler.normalize(q)
@@ -1105,6 +1151,23 @@ async def test_coding_dna_deletion(test_handler, coding_dna_deletion):
     assertion_checks(resp.variation_descriptor, coding_dna_deletion, q)
 
 
+@pytest.mark.asyncio
+async def test_genomic_deletion(test_handler, genomic_deletion):
+    """Test that genomic deletion normalizes correctly"""
+    # CA915940709
+    q = "NC_000003.12:g.10146527_10146528del"
+    resp1 = await test_handler.normalize(q)
+    assertion_checks(resp1.variation_descriptor, genomic_deletion, q)
+
+    resp2 = await test_handler.normalize("NC_000003.12:g.10146527_10146528delCT")
+    assert resp1.variation_descriptor.variation.id == \
+        resp2.variation_descriptor.variation.id
+
+    # incorrect deleted sequence
+    resp = await test_handler.normalize("NC_000003.12:g.10146527_10146528delCC")
+    assert not resp.variation_descriptor
+
+
 @pytest.mark.asyncio
 async def test_protein_insertion(test_handler, protein_insertion):
     """Test that protein insertion normalizes correctly."""
@@ -1214,6 +1277,21 @@ async def test_valid_queries(test_handler):
     assert resp.variation_descriptor.variation.id == \
         "ga4gh:VA.M0oqztcpIsGcwxeOfxR32Q9_2Xvpu4BE"
 
+    resp = await test_handler.normalize("NG_008212.3:g.5426_5445del")
+    assert resp.variation_descriptor
+
+    # Test ambiguous IUPAC code N
+    for q in [
+        "NC_000017.10:g.7572948_7572949insTTTTTTTTTNNNNN",
+        "NC_000007.13:g.140453136A>N",
+        "NC_000007.13:g.140453135_140453136delinsATN",
+        "NM_007294.3:c.2902_2903insTCN",
+        "NM_004333.4:c.1799T>N",
+        "NM_001289937.1:c.2326_2327delinsCTN"
+    ]:
+        resp = await test_handler.normalize(q)
+        assert resp.variation_descriptor, q
+
 
 @pytest.mark.asyncio
 async def test_no_matches(test_handler):