Merge pull request #286 from cancervariants/issue-285

feat: Add endpoint for parsed clinvar copy number gain/loss

tests/test_parsed_to_abs_cnv.py

@@ -0,0 +1,268 @@
+"""Test that parsed_to_abs_cnv works correctly"""
+import pytest
+from ga4gh.vrsatile.pydantic.vrs_models import AbsoluteCopyNumber
+
+from variation.schemas.service_schema import ClinVarAssembly
+
+
+@pytest.fixture(scope="module")
+def copy_number_gain1():
+    """Create test fixture for clinvar copy number gain.
+    https://www.ncbi.nlm.nih.gov/clinvar/variation/145208/?new_evidence=true
+    """
+    variation = {
+        "type": "AbsoluteCopyNumber",
+        "id": "ga4gh:VAC.accZJeJtNj0Zqv7KVqkT87ClTlg-4nwa",
+        "subject": {
+            "type": "SequenceLocation",
+            "id": "ga4gh:VSL.JTsxd9PiPZaIPL9Tl3ss78GYYnDeogvf",
+            "sequence_id": "ga4gh:SQ.S_KjnFVz-FE7M0W6yoaUDgYxLPc1jyWU",
+            "interval": {
+                "type": "SequenceInterval",
+                "start": {
+                    "type": "IndefiniteRange",
+                    "value": 143134062,
+                    "comparator": "<="
+                },
+                "end": {
+                    "type": "IndefiniteRange",
+                    "value": 143284670,
+                    "comparator": ">="
+                }
+            }
+        },
+        "copies": {"type": "Number", "value": 3}
+    }
+    return AbsoluteCopyNumber(**variation)
+
+
+@pytest.fixture(scope="module")
+def copy_number_gain2():
+    """Create test fixture for clinvar copy number gain.
+    https://www.ncbi.nlm.nih.gov/clinvar/variation/146181/?new_evidence=true
+    """
+    variation = {
+        "type": "AbsoluteCopyNumber",
+        "id": "ga4gh:VAC.oTO2JUsQdoJ2fudae5uO5uVNvIu7oA8m",
+        "subject": {
+            "type": "SequenceLocation",
+            "id": "ga4gh:VSL.9moblqAMqfEryr9pRUxqZMiOkqbsy5Ml",
+            "sequence_id": "ga4gh:SQ.AsXvWL1-2i5U_buw6_niVIxD6zTbAuS6",
+            "interval": {
+                "type": "SequenceInterval",
+                "start": {
+                    "type": "IndefiniteRange",
+                    "value": 31738808,
+                    "comparator": "<="
+                },
+                "end": {
+                    "type": "IndefiniteRange",
+                    "value": 32217725,
+                    "comparator": ">="
+                }
+            }
+        },
+        "copies": {"type": "Number", "value": 2}
+    }
+    return AbsoluteCopyNumber(**variation)
+
+
+@pytest.fixture(scope="module")
+def copy_number_loss1():
+    """Create test fixture for clinvar copy number loss.
+    https://www.ncbi.nlm.nih.gov/clinvar/variation/146181/?new_evidence=true
+    """
+    variation = {
+        "type": "AbsoluteCopyNumber",
+        "id": "ga4gh:VAC.5QpagPqyrE4vUigmRi58NrPmPhQsI7kM",
+        "subject": {
+            "type": "SequenceLocation",
+            "id": "ga4gh:VSL.Szlw1t4YMuaO7lLwFJ-T7fGTcXuhNNKB",
+            "sequence_id": "ga4gh:SQ.v7noePfnNpK8ghYXEqZ9NukMXW7YeNsm",
+            "interval": {
+                "type": "SequenceInterval",
+                "start": {
+                    "type": "IndefiniteRange",
+                    "value": 10491131,
+                    "comparator": "<="
+                },
+                "end": {
+                    "type": "IndefiniteRange",
+                    "value": 10535643,
+                    "comparator": ">="
+                }
+            }
+        },
+        "copies": {"type": "Number", "value": 1}
+    }
+    return AbsoluteCopyNumber(**variation)
+
+
+@pytest.fixture(scope="module")
+def copy_number_loss2():
+    """Create test fixture for clinvar copy number loss.
+    https://www.ncbi.nlm.nih.gov/clinvar/variation/148425/?new_evidence=true
+    """
+    variation = {
+        "type": "AbsoluteCopyNumber",
+        "id": "ga4gh:VAC.ZWN8WnEksqBj4bKFIB60Wag6hGeeobB5",
+        "subject": {
+            "type": "SequenceLocation",
+            "id": "ga4gh:VSL.Bp-86GeYti1DBmrj_Dtz7qNIMF5ygx5y",
+            "sequence_id": "ga4gh:SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5",
+            "interval": {
+                "type": "SequenceInterval",
+                "start": {
+                    "type": "IndefiniteRange",
+                    "value": 10000,
+                    "comparator": "<="
+                },
+                "end": {
+                    "type": "IndefiniteRange",
+                    "value": 1223133,
+                    "comparator": ">="
+                }
+            }
+        },
+        "copies": {"type": "Number", "value": 0}
+    }
+    return AbsoluteCopyNumber(**variation)
+
+
+def test_parsed_copy_number_gain(test_query_handler, copy_number_gain1,
+                                 copy_number_gain2):
+    """Test that parsed_to_abs_cnv works for parsed copy number gain queries"""
+    # https://www.ncbi.nlm.nih.gov/clinvar/variation/145208/?new_evidence=true
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        143134063, 143284670, 3, assembly="GRCh37", chr="chr1")
+    assert resp.dict() == copy_number_gain1.dict()
+    assert w == []
+
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        143134063, 143284670, 3, assembly="hg19", chr="chr1")
+    assert resp.dict() == copy_number_gain1.dict()
+    assert w == []
+
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        143134063, 143284670, 3, accession="NC_000001.10")
+    assert resp.dict() == copy_number_gain1.dict()
+    assert w == []
+
+    # https://www.ncbi.nlm.nih.gov/clinvar/variation/146181/?new_evidence=true
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        31738809, 32217725, 2, assembly="GRCh38", chr="chr15")
+    assert resp.dict() == copy_number_gain2.dict()
+    assert w == []
+
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        31738809, 32217725, 2, assembly="GRCh38", chr="15")
+    assert resp.dict() == copy_number_gain2.dict()
+    assert w == []
+
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        31738809, 32217725, 2, assembly="hg38", chr="chr15")
+    assert resp.dict() == copy_number_gain2.dict()
+    assert w == []
+
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        31738809, 32217725, 2, accession="NC_000015.10")
+    assert resp.dict() == copy_number_gain2.dict()
+    assert w == []
+
+
+def test_parsed_copy_number_loss(test_query_handler, copy_number_loss1,
+                                 copy_number_loss2):
+    """Test that parsed_to_abs_cnv works for parsed copy number loss queries"""
+    # https://www.ncbi.nlm.nih.gov/clinvar/variation/1299222/?new_evidence=true
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        10491132, 10535643, 1, assembly=ClinVarAssembly.GRCH37, chr="chrX")
+    assert resp.dict() == copy_number_loss1.dict()
+    assert w == []
+
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        10491132, 10535643, 1, assembly=ClinVarAssembly.HG19, chr="chrX")
+    assert resp.dict() == copy_number_loss1.dict()
+    assert w == []
+
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        10491132, 10535643, 1, assembly=ClinVarAssembly.HG19, chr="X")
+    assert resp.dict() == copy_number_loss1.dict()
+    assert w == []
+
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        10491132, 10535643, 1, accession="NC_000023.10")
+    assert resp.dict() == copy_number_loss1.dict()
+    assert w == []
+
+    # https://www.ncbi.nlm.nih.gov/clinvar/variation/148425/?new_evidence=true
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        10001, 1223133, 0, assembly=ClinVarAssembly.GRCH38, chr="chrY")
+    assert resp.dict() == copy_number_loss2.dict()
+    assert w == []
+
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        10001, 1223133, 0, assembly=ClinVarAssembly.HG38, chr="chrY")
+    assert resp.dict() == copy_number_loss2.dict()
+    assert w == []
+
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        10001, 1223133, 0, accession="NC_000024.10")
+    assert resp.dict() == copy_number_loss2.dict()
+    assert w == []
+
+
+def test_invalid(test_query_handler):
+    """Test invalid queries returns Text variation and warnings"""
+    # NCBI36/hg18 assembly
+    # https://www.ncbi.nlm.nih.gov/clinvar/variation/443961/?new_evidence=true
+    expected_w = ["NCBI36 assembly is not current supported"]
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        2623228, 3150942, 3, assembly=ClinVarAssembly.NCBI36, chr="chr1")
+    assert resp.type == "Text"
+    assert w == expected_w
+
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        2623228, 3150942, 3, assembly=ClinVarAssembly.HG18, chr="chr1")
+    assert resp.type == "Text"
+    assert w == expected_w
+
+    # Must give both assembly + chr or accession
+    expected_w = ["Must provide either `accession` or both `assembly` and `chr`."]
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        31738809, 32217725, 2, assembly="hg38")
+    assert resp.type == "Text"
+    assert w == expected_w
+
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        31738809, 32217725, 2, chr="chr15")
+    assert resp.type == "Text"
+    assert w == expected_w
+
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        31738809, 32217725, 2)
+    assert resp.type == "Text"
+    assert w == expected_w
+
+    # invalid chr
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        10001, 1223133, 0, assembly=ClinVarAssembly.GRCH38, chr="z")
+    assert resp.type == "Text"
+    assert w == ["SeqRepo unable to get translated identifiers for GRCh38:z"]
+
+    # invalid assembly
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        10001, 1223133, 0, assembly="GRCh99", chr="Y")
+    assert resp.type == "Text"
+    assert w == ["SeqRepo unable to get translated identifiers for GRCh99:Y"]
+
+    # invalid accession
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        10491132, 10535643, 1, accession="NC_00002310")
+    assert resp.type == "Text"
+    assert w == ["NC_00002310 does not exist in SeqRepo"]
+
+    # Invalid position
+    resp, w = test_query_handler.parsed_to_abs_cnv(
+        31738809, 2302991250, 2, accession="NC_000015.10")
+    assert resp.type == "Text"
+    assert w == ["Position out of range (2302991250)"]

variation/main.py

@@ -19,6 +19,8 @@
 from variation.schemas.normalize_response_schema \
     import HGVSDupDelMode as HGVSDupDelModeEnum, ToCanonicalVariationFmt, \
     ToCanonicalVariationService, TranslateIdentifierService
+from variation.schemas.service_schema import ClinVarAssembly, ParsedToAbsCnvQuery, \
+    ParsedToAbsCnvService
 from .version import __version__
 from .schemas.vrs_python_translator_schema import TranslateFromFormat, \
     TranslateFromService, TranslateFromQuery, VrsPythonMeta
@@ -502,3 +504,59 @@ async def hgvs_to_relative_copy_number(
         ),
         relative_copy_number=variation
     )
+
+
+assembly_descr = "Assembly. If `accession` is set, will ignore `assembly` and `chr`. "\
+                 "If `accession` not set, must provide both `assembly` and `chr`."
+chr_descr = "Chromosome. Must set when `assembly` is set."
+accession_descr = "Accession. If `accession` is set, will ignore `assembly` and "\
+                  "`chr`. If `accession` not set, must provide both `assembly` and `chr`."  # noqa: E501
+start_descr = "Start position as residue coordinate"
+end_descr = "End position as residue coordinate"
+total_copies_descr = "Total copies for Absolute Copy Number variation object"
+
+
+@app.get("/variation/parsed_to_abs_cnv",
+         summary="Given parsed ClinVar Copy Number Gain/Loss components, return "
+         "absolute copy number variation",
+         response_description="A response to a validly-formed query.",
+         description="Return VRS Absolute Copy Number Variation",
+         response_model=ParsedToAbsCnvService,
+         tags=[Tags.TO_COPY_NUMBER_VARIATION]
+         )
+def parsed_to_abs_cnv(
+    assembly: Optional[ClinVarAssembly] = Query(None, description=assembly_descr),
+    chr: Optional[str] = Query(None, description=chr_descr),
+    accession: Optional[str] = Query(None, description=accession_descr),
+    start: int = Query(..., description=start_descr),
+    end: int = Query(..., description=end_descr),
+    total_copies: int = Query(..., description=total_copies_descr)
+) -> ParsedToAbsCnvService:
+    """Given parsed ClinVar Copy Number Gain/Loss components, return Absolute
+    Copy Number Variation
+
+    :param int start: Start position as residue coordinate
+    :param int end: End position as residue coordinate
+    :param int total_copies: Total copies for Absolute Copy Number variation object
+    :param Optional[ClinVarAssembly] assembly: Assembly. If `accession` is set,
+        will ignore `assembly` and `chr`. If `accession` not set, must provide
+        both `assembly` and `chr`.
+    :param Optional[str] chr: Chromosome. Must set when `assembly` is set.
+    :param Optional[str] accession: Accession. If `accession` is set,
+        will ignore `assembly` and `chr`. If `accession` not set, must provide
+        both `assembly` and `chr`.
+    :return: Tuple containing Absolute Copy Number variation and list of warnings
+    """
+    variation, warnings = query_handler.parsed_to_abs_cnv(
+        start, end, total_copies, assembly, chr, accession)
+    query = ParsedToAbsCnvQuery(assembly=assembly, chr=chr, accession=accession,
+                                start=start, end=end, total_copies=total_copies)
+    return ParsedToAbsCnvService(
+        query=query,
+        absolute_copy_number=variation,
+        warnings=warnings,
+        service_meta_=ServiceMeta(
+            version=__version__,
+            response_datetime=datetime.now()
+        )
+    )