loqusdb 2.7.11__py3-none-any.whl → 2.7.12__py3-none-any.whl

tests/conftest.py

@@ -1,438 +0,0 @@
-import logging
-
-import cyvcf2
-import pytest
-
-from loqusdb.build_models.case import build_case
-from loqusdb.build_models.variant import build_variant
-from loqusdb.log import init_log
-from loqusdb.models import Case
-from loqusdb.plugins.mongo.adapter import MongoAdapter
-from loqusdb.utils.load import update_case
-from mongomock import MongoClient as MockClient
-from ped_parser import FamilyParser
-from pymongo import MongoClient
-
-logger = logging.getLogger(".")
-
-init_log(logger, loglevel="DEBUG")
-
-REAL_DATABASE = "loqus-test"
-TEST_DATABASE = "test"
-
-
-class CyvcfVariant(object):
-    """Mock a cyvcf variant
-
-    Default is to return a variant with three individuals high genotype
-    quality.
-    """
-
-    def __init__(
-        self,
-        chrom="1",
-        pos=80000,
-        ref="A",
-        alt="C",
-        end=None,
-        gt_quals=[60, 60, 60],
-        gt_types=[1, 1, 0],
-        var_type="snv",
-        var_id=None,
-        info_dict={},
-    ):
-        super(CyvcfVariant, self).__init__()
-        self.CHROM = chrom
-        self.POS = pos
-        self.REF = ref
-        self.ALT = [alt]
-        self.end = end or pos
-        self.gt_quals = gt_quals
-        self.gt_types = gt_types
-        self.var_type = var_type
-        self.INFO = info_dict
-        if var_id is None:
-            var_id = "."
-        self.ID = var_id
-
-
-@pytest.fixture(scope="function")
-def real_db_name(request):
-    """Return the name of the real mongo test db"""
-    return REAL_DATABASE
-
-
-@pytest.fixture(scope="function")
-def mongo_client(request):
-    """Return a mongomock client"""
-    client = MockClient(directConnection=True)
-    return client
-
-
-@pytest.fixture(scope="function")
-def real_mongo_client(request):
-    """Return a mongomock client"""
-    client = MongoClient(directConnection=True)
-
-    def teardown():
-        print("\n")
-        logger.info("Deleting database")
-        client.drop_database(REAL_DATABASE)
-        logger.info("Database deleted")
-
-    request.addfinalizer(teardown)
-
-    return client
-
-
-@pytest.fixture(scope="function")
-def mongo_adapter(request, mongo_client):
-    """Return a mongo adapter"""
-    db_name = TEST_DATABASE
-    adapter = MongoAdapter(mongo_client, db_name)
-
-    return adapter
-
-
-@pytest.fixture(scope="function")
-def real_mongo_adapter(request, real_mongo_client):
-    """Return a mongo adapter"""
-    db_name = REAL_DATABASE
-    adapter = MongoAdapter(real_mongo_client, db_name)
-
-    return adapter
-
-
-@pytest.fixture(scope="function")
-def simplest_variant(request):
-    variant = {
-        "_id": "test",
-    }
-    return variant
-
-
-@pytest.fixture(scope="function")
-def homozygous_variant(request):
-    variant = {"_id": "test", "homozygote": 1, "case_id": "1"}
-    return variant
-
-
-@pytest.fixture(scope="function")
-def simple_case(request):
-    case = Case("test", "./test.vcf")
-
-    return case
-
-
-@pytest.fixture(scope="function")
-def vcf_path(request):
-    file_path = "tests/fixtures/test.vcf"
-    return file_path
-
-
-@pytest.fixture(scope="function")
-def sv_vcf_path(request):
-    file_path = "tests/fixtures/test.SV.vcf"
-    return file_path
-
-
-@pytest.fixture(scope="function")
-def double_vcf_path(request):
-    "This will return a vcf with the same variant two times"
-    file_path = "tests/fixtures/double_variant.vcf"
-    return file_path
-
-
-@pytest.fixture(scope="function")
-def unsorted_vcf_path(request):
-    "This will return a vcf with unsorted variants"
-    file_path = "tests/fixtures/unsorted.vcf"
-    return file_path
-
-
-@pytest.fixture(scope="function")
-def zipped_vcf_path(request):
-    "Returns a VCF that is gzipped and have a index companion"
-    file_path = "tests/fixtures/test.vcf.gz"
-    return file_path
-
-
-@pytest.fixture(scope="function")
-def profile_vcf_path(request):
-    "Returns a VCF containing profile variants"
-    file_path = "tests/fixtures/profile_snv.vcf"
-    return file_path
-
-
-@pytest.fixture(scope="function")
-def ped_path(request):
-    file_path = "tests/fixtures/recessive_trio.ped"
-    return file_path
-
-
-@pytest.fixture(scope="function")
-def funny_ped_path(request):
-    "Returns a ped file with incorrect family relations"
-    return "tests/fixtures/funny_trio.ped"
-
-
-@pytest.fixture(scope="function")
-def ind_positions(request):
-    return {"proband": 0, "mother": 1, "father": 2}
-
-
-@pytest.fixture(scope="function")
-def case_lines(request, ped_path):
-    """Return ped formated case lines"""
-    case = []
-    with open(ped_path, "r") as f:
-        for line in f:
-            case.append(line)
-
-    return case
-
-
-@pytest.fixture(scope="function")
-def case_id(request, ped_path):
-    """Return ped formated case lines"""
-    case_id = None
-    with open(ped_path, "r") as f:
-        for line in f:
-            case_id = line.split("\t")[0]
-
-    return case_id
-
-
-@pytest.fixture(scope="function")
-def vcf_obj(request, vcf_path):
-    """return a cyvcf2.VCF obj"""
-    return cyvcf2.VCF(vcf_path)
-
-
-@pytest.fixture(scope="function")
-def sv_vcf_obj(request, sv_vcf_path):
-    """return a cyvcf2.VCF obj"""
-    return cyvcf2.VCF(sv_vcf_path)
-
-
-@pytest.fixture(scope="function")
-def profile_list(request):
-    return ["AA", "CC", "GG", "TT"]
-
-
-@pytest.fixture(scope="function")
-def case_obj(request, case_lines, vcf_obj, vcf_path, profile_list):
-    """Return a case obj"""
-    family_parser = FamilyParser(case_lines, family_type="ped")
-    families = list(family_parser.families.keys())
-    family = family_parser.families[families[0]]
-    vcf_individuals = vcf_obj.samples
-    nr_variants = 0
-    for nr_variants, variant in enumerate(vcf_obj, 1):
-        continue
-    return build_case(
-        case=family,
-        vcf_individuals=vcf_individuals,
-        vcf_path=vcf_path,
-        nr_variants=nr_variants,
-        profiles={individual: profile_list for individual in vcf_individuals},
-    )
-
-
-@pytest.fixture(scope="function")
-def sv_case_obj(request, case_lines, sv_vcf_obj, sv_vcf_path):
-    """Return a case obj"""
-    family_parser = FamilyParser(case_lines, family_type="ped")
-    families = list(family_parser.families.keys())
-    family = family_parser.families[families[0]]
-    vcf_individuals = sv_vcf_obj.samples
-    nr_variants = 0
-    for nr_variants, variant in enumerate(sv_vcf_obj, 1):
-        continue
-    return build_case(
-        case=family,
-        sv_individuals=vcf_individuals,
-        vcf_sv_path=sv_vcf_path,
-        nr_sv_variants=nr_variants,
-    )
-
-
-@pytest.fixture(scope="function")
-def complete_case_obj(request, case_obj, sv_case_obj):
-    """Return a case obj with both sv and snv information"""
-    return update_case(case_obj, sv_case_obj)
-
-
-@pytest.fixture(scope="function")
-def family_obj(request, case_lines):
-    """Return a case obj"""
-    family_parser = FamilyParser(case_lines, family_type="ped")
-    families = list(family_parser.families.keys())
-    return family_parser.families[families[0]]
-
-
-@pytest.fixture(scope="function")
-def case_id(request, case_lines):
-    """Return a case id"""
-    family_parser = FamilyParser(case_lines, family_type="ped")
-    families = list(family_parser.families.keys())
-    family = family_parser.families[families[0]]
-    return family.family_id
-
-
-@pytest.fixture(scope="function")
-def individuals(request, case_obj):
-    """Return a case obj"""
-
-    return case_obj.individuals
-
-
-@pytest.fixture(scope="function")
-def two_cases(request):
-    """Return ped formated case lines"""
-    return [
-        "#FamilyID\tSampleID\tFather\tMother\tSex\tPhenotype\n",
-        "1\tproband\t0\t0\t1\t2\n",
-        "2\tproband\t0\t0\t2\t1\n",
-    ]
-
-
-## Variant fixtures:
-
-# chrom='1',
-# pos=80000,
-# ref='A',
-# alt='C',
-# end=None,
-# gt_quals=[60, 60, 60],
-# gt_types=[1, 1, 0],
-# var_type='snv',
-# info_dict={}
-
-### Variant objects
-
-
-@pytest.fixture(scope="function")
-def variant_obj(request, het_variant, ind_positions, individuals):
-    return build_variant(
-        variant=het_variant,
-        individuals=individuals,
-        ind_positions=ind_positions,
-        case_id="test",
-        gq_threshold=None,
-    )
-
-
-### CYVCF2 variants
-### SNVs:
-@pytest.fixture(scope="function")
-def hem_variant(request):
-    return CyvcfVariant(chrom="X", pos=60000)
-
-
-@pytest.fixture(scope="function")
-def variant_chr(request):
-    return CyvcfVariant(chrom="chrX", pos=60000)
-
-
-@pytest.fixture(scope="function")
-def par_variant(request):
-    return CyvcfVariant(chrom="X", pos=60001)
-
-
-@pytest.fixture(scope="function")
-def het_variant(request):
-    return CyvcfVariant()
-
-
-@pytest.fixture(scope="function")
-def bnd_variant(request):
-    return CyvcfVariant(
-        chrom="1",
-        pos=80000,
-        alt="N[1:80000[",
-        ref="N",
-        end=80000,
-        info_dict={"SVTYPE": "BND"},
-    )
-
-
-@pytest.fixture(scope="function")
-def variant_no_gq(request):
-    return CyvcfVariant(gt_quals=[-1, -1, -1])
-
-
-@pytest.fixture(scope="function")
-def hom_variant(request):
-    return CyvcfVariant(gt_types=[3, 1, 1])
-
-
-@pytest.fixture(scope="function")
-def variant_no_call(request):
-    return CyvcfVariant(gt_types=[2, 2, 2])
-
-
-### SVs:
-@pytest.fixture(scope="function")
-def del_variant(request):
-    return CyvcfVariant(
-        chrom="1",
-        ref="G",
-        alt="<DEL>",
-        pos=1285001,
-        end=1287000,
-        var_type="sv",
-        info_dict={"END": 1287000, "SVLEN": -20000, "SVTYPE": "DEL"},
-    )
-
-
-@pytest.fixture(scope="function")
-def small_insert_variant(request):
-    return CyvcfVariant(
-        chrom="1",
-        ref="G",
-        alt="GGGACGGGGGTTCTGAGATAAGCAAGCCCCCACCAGGTGAGACCGGCGGAGCTGTGGCCACCGAGGTCCCGGGAGCTGGTGCT",
-        pos=3021145,
-        end=3021145,
-        var_type="sv",
-        info_dict={"END": 3021145, "SVLEN": 82, "SVTYPE": "INS"},
-    )
-
-
-@pytest.fixture(scope="function")
-def insertion_variant(request):
-    return CyvcfVariant(
-        chrom="1",
-        ref="A",
-        alt="<INS>",
-        pos=3177306,
-        end=3177306,
-        var_type="sv",
-        info_dict={"END": 3177306, "SVLEN": None, "SVTYPE": "INS"},
-    )
-
-
-@pytest.fixture(scope="function")
-def duptandem_variant(request):
-    return CyvcfVariant(
-        chrom="1",
-        ref="A",
-        alt="<DUP:TANDEM>",
-        pos=3092626,
-        end=3092849,
-        var_type="sv",
-        info_dict={"END": 3092849, "SVLEN": 223, "SVTYPE": "DUP"},
-    )
-
-
-@pytest.fixture(scope="function")
-def translocation_variant(request):
-    return CyvcfVariant(
-        chrom="1",
-        ref="N",
-        alt="N[11:119123896[",
-        pos=3754913,
-        end=3754913,
-        var_type="sv",
-        info_dict={"END": None, "SVLEN": None, "SVTYPE": "BND"},
-    )