loqusdb 2.7.10__py3-none-any.whl → 2.7.11__py3-none-any.whl

loqusdb/__init__.py

@@ -4,7 +4,7 @@ from pymongo import ASCENDING, IndexModel
 
 logger = logging.getLogger(__name__)
 
-__version__ = "2.7.10"
+__version__ = "2.7.11"
 
 INDEXES = {
     "variant": [

loqusdb/build_models/variant.py

@@ -1,10 +1,9 @@
 import logging
 from collections import namedtuple
+from typing import Optional
 
 import cyvcf2
 
-from typing import Optional
-
 from loqusdb.constants import CHROM_TO_INT, GENOTYPE_MAP, GRCH37, PAR
 from loqusdb.models import Case, Variant
 
@@ -143,7 +142,14 @@ def get_coords(variant):
     return coordinates
 
 
-def build_variant(variant: cyvcf2.Variant, case_obj: Case, case_id: Optional[str]=None, gq_threshold: Optional[int]=None, gq_qual: Optional[bool]=False, genome_build: Optional[str]=None) -> Variant:
+def build_variant(
+    variant: cyvcf2.Variant,
+    case_obj: Case,
+    case_id: Optional[str] = None,
+    gq_threshold: Optional[int] = None,
+    gq_qual: Optional[bool] = False,
+    genome_build: Optional[str] = None,
+) -> Variant:
     """Return a Variant object
 
     Take a cyvcf2 formated variant line and return a models.Variant.
@@ -191,7 +197,6 @@ def build_variant(variant: cyvcf2.Variant, case_obj: Case, case_id: Optional[str
     else:
         found_variant = False
         for ind_obj in case_obj["individuals"]:
-            ind_id = ind_obj["ind_id"]
             # Get the index position for the individual in the VCF
             ind_pos = ind_obj["ind_index"]
 

loqusdb/commands/load.py

@@ -3,10 +3,10 @@ import os
 from datetime import datetime
 
 import click
-from loqusdb.exceptions import CaseError
-from loqusdb.utils.load import load_database
 
 from loqusdb.commands.cli import cli as base_command
+from loqusdb.exceptions import CaseError
+from loqusdb.utils.load import load_database
 
 LOG = logging.getLogger(__name__)
 
@@ -55,7 +55,13 @@ def validate_profile_threshold(ctx, param, value):
 )
 @click.option("--ensure-index", is_flag=True, help="Make sure that the indexes are in place")
 @click.option("--gq-threshold", default=20, show_default=True, help="Threshold to consider variant")
-@click.option("--qual-gq", is_flag=True, default=False, show_default=True, help="Use QUAL tag instead of GQ value for quality filter")
+@click.option(
+    "--qual-gq",
+    is_flag=True,
+    default=False,
+    show_default=True,
+    help="Use QUAL tag instead of GQ value for quality filter",
+)
 @click.option(
     "--max-window",
     "-m",
@@ -97,7 +103,7 @@ def load(
     check_profile,
     hard_threshold,
     soft_threshold,
-    qual_gq
+    qual_gq,
 ):
     """Load the variants of a case
 

loqusdb/commands/view.py

@@ -2,9 +2,9 @@
 import json
 import logging
 from pprint import pprint as pp
-from pymongo.cursor import Cursor
 
 import click
+from pymongo.cursor import Cursor
 
 from loqusdb.commands.cli import cli as base_command
 
@@ -49,7 +49,6 @@ def cases(ctx, case_id, to_json, count, case_type):
             ctx.abort()
         cases: Cursor = adapter.cases()
 
-
     if to_json:
         click.echo(json.dumps(cases))
         return

loqusdb/plugins/mongo/structural_variant.py

@@ -1,8 +1,9 @@
 import logging
 
-from loqusdb.models import Identity
 from pymongo import ASCENDING
 
+from loqusdb.models import Identity
+
 LOG = logging.getLogger(__name__)
 
 
@@ -175,7 +176,6 @@ class SVMixin:
         self.db.identity.delete_one(dict(identity_obj))
 
     def _update_sv_metrics(self, sv_type, pos_mean, end_mean, max_window):
-
         """
         calculates cluster length, and interval size for SV based on
         mean start position and mean end position.

loqusdb/utils/load.py

@@ -11,15 +11,14 @@ import logging
 
 import click
 
+from loqusdb.build_models.case import build_case
+from loqusdb.build_models.profile_variant import build_profile_variant
+from loqusdb.build_models.variant import build_variant
 from loqusdb.exceptions import CaseError, VcfError
-
 from loqusdb.utils.case import get_case, update_case
 from loqusdb.utils.delete import delete
 from loqusdb.utils.profiling import get_profiles, profile_match
 from loqusdb.utils.vcf import check_vcf, get_vcf
-from loqusdb.build_models.case import build_case
-from loqusdb.build_models.profile_variant import build_profile_variant
-from loqusdb.build_models.variant import build_variant
 
 LOG = logging.getLogger(__name__)
 
@@ -226,7 +225,9 @@ def load_variants(
     with click.progressbar(vcf_obj, label="Inserting variants", length=nr_variants) as bar:
 
         variants = (
-            build_variant(variant, case_obj, case_id, gq_threshold, qual_gq, genome_build=genome_build)
+            build_variant(
+                variant, case_obj, case_id, gq_threshold, qual_gq, genome_build=genome_build
+            )
             for variant in bar
         )
 
@@ -258,7 +259,6 @@ def load_profile_variants(adapter, variant_file):
     """
 
     vcf_info = check_vcf(variant_file)
-    nr_variants = vcf_info["nr_variants"]
     variant_type = vcf_info["variant_type"]
 
     if variant_type != "snv":

loqusdb/utils/variant.py

@@ -32,14 +32,13 @@ def format_info(variant, variant_type="snv", nr_cases=None, add_freq=False):
 
     # This is SV specific
     if variant_type == "sv":
-        pos= int((variant["pos_left"] + variant["pos_right"]) / 2)
+        pos = int((variant["pos_left"] + variant["pos_right"]) / 2)
         end = int((variant["end_left"] + variant["end_right"]) / 2)
 
-        if not variant['sv_type'] == "BND":
+        if not variant["sv_type"] == "BND":
             vcf_info += f";SVTYPE={variant['sv_type']};END={end};SVLEN={variant['length']}"
         else:
-            vcf_info += f";SVTYPE=BND"
-
+            vcf_info += ";SVTYPE=BND"
 
     return vcf_info
 
@@ -63,10 +62,10 @@ def format_variant(variant, variant_type="snv", nr_cases=None, add_freq=False):
 
     if variant_type == "sv":
         pos = int((variant["pos_left"] + variant["pos_right"]) / 2)
-        end=  int((variant["end_left"] + variant["end_right"]) / 2)
+        end = int((variant["end_left"] + variant["end_right"]) / 2)
         ref = "N"
 
-        if not variant['sv_type'] == "BND":
+        if not variant["sv_type"] == "BND":
             alt = f"<{variant['sv_type']}>"
         else:
             alt = f"N]{variant['end_chrom']}:{end}]"

{loqusdb-2.7.10.dist-info → loqusdb-2.7.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: loqusdb
-Version: 2.7.10
+Version: 2.7.11
 Summary: A simple observation count database
 License: MIT
 Author: Your Name

{loqusdb-2.7.10.dist-info → loqusdb-2.7.11.dist-info}/RECORD

@@ -1,22 +1,22 @@
 README.md,sha256=0-XD0EEYvCnenT07wkO0ZX6lJbzN8OC1cV3M9G47nps,4648
-loqusdb/__init__.py,sha256=kpB-4LlsICY9AfcuMV_bs-94IjgIkzfQr9yfPJizESk,1688
+loqusdb/__init__.py,sha256=tVCT5pNoMl8Zuqcc32Dbade0bG0SS7s05LMGyRM2gL0,1688
 loqusdb/__main__.py,sha256=8FGKySAGaWSzAYMj6HRsxeyiME3V01Idt7HrmN7pSYY,397
 loqusdb/build_models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 loqusdb/build_models/case.py,sha256=AByutEYK2N3kS9JFvyZfPKNZdCpZHCSD0nNHAgaU1Cs,4127
 loqusdb/build_models/profile_variant.py,sha256=TbSxfVjESstS_FgbkOW4NQwMQVeTyhn9oc9yPZmDhzI,1021
-loqusdb/build_models/variant.py,sha256=LviEaovB_s_-jaLM64x0NzqzilFr__NPgv4Vf49Rhbk,6939
+loqusdb/build_models/variant.py,sha256=2ate8viYhHK1yX7UvCzEPgfuuXwTgAApU_2E5jl1ZO4,6934
 loqusdb/commands/__init__.py,sha256=BXAN3UADgqPrkGczzjlLO9GyyQ96dnLnP7n92JlYHgo,603
 loqusdb/commands/annotate.py,sha256=748kImopE5WbaO1nuv3WUgIqezWFSsi7SBeWhOz26-s,1384
 loqusdb/commands/cli.py,sha256=wJD5S1BoCxtRTAobd1QtmQpzlngJg-mt1nsyD92fDD4,3176
 loqusdb/commands/delete.py,sha256=R6ysHKSMw1mmL4ZbktoUIKzdzDLQ3314YPYhIy1myic,1979
 loqusdb/commands/export.py,sha256=-9SHgvr0G8FlyW0FGSfe1dmNDnjx4HKAaa-xYzSkvNc,3238
 loqusdb/commands/identity.py,sha256=KLA9c8e6cJFDxtqIa1G6zdHTHK1sz2b3v1Utdtik_4k,787
-loqusdb/commands/load.py,sha256=cVDdY7meBfcv8nMEGsjAX6aE-SKDOceGqM2vAvXPhko,4407
+loqusdb/commands/load.py,sha256=sDGCOGbukdfebLn1iBGyWoI6t3tijLzywP1tg3WheQI,4431
 loqusdb/commands/load_profile.py,sha256=cflCbF9f77_HCH8xPnN8zSSocvIffRMnC2LPE0j7Xq8,3336
 loqusdb/commands/migrate.py,sha256=2C8YL-zVqnpnqg3JIyUr0rbVnb8-AGPVWNhicHnPKLo,667
 loqusdb/commands/restore.py,sha256=eqPX0yao0IAYS5SbjCdlsfSJRBbRByBLISUU2hTzqqs,1492
 loqusdb/commands/update.py,sha256=zz3wueaJVqJ1FKact-rpY2az__5oa1LnZKf7mgqNGPk,3211
-loqusdb/commands/view.py,sha256=kQ_HuFhIX5wTHoEFC6atH-5unQFkRtopzD2_GqHNPKY,5198
+loqusdb/commands/view.py,sha256=PkwyvzQgq5ArrEakI-lKQThrhjBLLl2gYejHI2g13WU,5197
 loqusdb/commands/wipe.py,sha256=WTOjyNooCUhtmZ6pdcPFa0PZrFc9E_pkLbnat_zP96M,553
 loqusdb/constants/__init__.py,sha256=r6y2TN8BqbKuh2Uyxq0trh-3A9xiWeStqWlvEPp-rSA,1645
 loqusdb/exceptions/__init__.py,sha256=Fq0UQg9TepWh19D7WT3dARyAHvorwJF6phhnZi2AkxE,88
@@ -34,7 +34,7 @@ loqusdb/plugins/mongo/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3h
 loqusdb/plugins/mongo/adapter.py,sha256=rRUQ2y_bZwjINbdTtfzJ_1JwE0Ns0usyAJ3o0O1Y10I,2593
 loqusdb/plugins/mongo/case.py,sha256=zKnaaam8Ey1AEH-1GofXp6iNqgmSvWWxZZWsx7dAO0Y,3006
 loqusdb/plugins/mongo/profile_variant.py,sha256=madOBa3HacIN_T1V8mp7NEC4QOpqQBqSY6pKTObkMLA,600
-loqusdb/plugins/mongo/structural_variant.py,sha256=RPc3GF37-O3GqRS9Z5PRxsBXACljfRT4KFsrEl0jCu0,12955
+loqusdb/plugins/mongo/structural_variant.py,sha256=7NjdRxRVzp4huTTEPI-buKoG7N5d_5LH11GHcncwboE,12955
 loqusdb/plugins/mongo/variant.py,sha256=NS3N8bhRap1b2ZSGjOw2LO6l7q_CzD00GZs499l38Tg,8715
 loqusdb/resources/__init__.py,sha256=JOx3Ppgtghx55cOJN0bfBonSXM5DM_v0OFdlT-Qybg4,639
 loqusdb/resources/loqusdb.20181005.gz,sha256=DI8CLI7fPnIAjM25Avraz-C7KQkOKsfnhgZWguGat9Y,12172904
@@ -44,18 +44,18 @@ loqusdb/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 loqusdb/utils/annotate.py,sha256=cPNWlhsv6yoe3lxNfa9DytO5eACuM_mOJJw_mglVMN0,2646
 loqusdb/utils/case.py,sha256=aeTvyACJTDjzl-aOjAZaUzFMLisgFKMfcoXSvNAZz4s,2168
 loqusdb/utils/delete.py,sha256=-ddBM_QXKzlUN6egEJggKzXX1P-WEdi92HgaD1DJRtg,4843
-loqusdb/utils/load.py,sha256=rujUk89lL5jO35QfO8NKGJkjEJmN6PQxohKkxtpnw6Y,8252
+loqusdb/utils/load.py,sha256=ZdsnmHTVGOjwG24Fm5gcUu7tcLwYSqvh3W9j6ixqyF0,8239
 loqusdb/utils/migrate.py,sha256=9Q6kdIi9TpFVzDYptlEE8RqPPS5wyzfM3F8egzmmBBk,1113
 loqusdb/utils/profiling.py,sha256=3OizF7CpYvSl9kyl2g4KGJxbIRUqWfmfLxn3843XYDk,9164
 loqusdb/utils/update.py,sha256=1edJG-u24FgOSxyXAQEiyTG4IyK-Uo3lSIl5qyzcXsI,4433
-loqusdb/utils/variant.py,sha256=Lq5x9egVB-3rExBiRceF67TaL4Hp2gGoWMSRBEcnm4Q,2088
+loqusdb/utils/variant.py,sha256=U6nMZRUf5NDDQ74nG0HBCLMnFQVgFAT6eHll_F2uiwc,2087
 loqusdb/utils/vcf.py,sha256=ybmrTBEPYa0FbUXo8ttlwATk13RnKjX9eIDbRDwCiVE,5175
 tests/build_models/test_build_case.py,sha256=4CzykSmiBgAVZWlqzjLTjBmY9NafzmPol7LiEu4003U,4404
 tests/build_models/test_build_variant.py,sha256=-9ulYBNBIxAGt_FiyaADWLuTJ4bWwRVVfMbjzummMZA,537
 tests/build_models/test_is_greater.py,sha256=sAz_UB6oGr72Pqc7ZEbPTw6N07E0QR-Yvn8UCEi0yP8,1360
-tests/commands/test_export.py,sha256=PGLtmxbOzEgWsS9AqAQkjBY9NlQiHdWfrt7DAPUSzrY,439
-tests/commands/test_identity.py,sha256=uEYPNkBvyQScrMRGpBqpINLDN3MgGt2nqXXjAkowQvc,566
-tests/commands/test_view.py,sha256=wUM5DXqDBs0OP-KsWh1_Lizhizvt5-GFawgOKgN4FDM,659
+tests/commands/test_export.py,sha256=Xdivbs_hDJzoJKNP60gnb6AgGfNdOqVTyk0lAkMFwPg,440
+tests/commands/test_identity.py,sha256=6yCD4m6ezGTsoW5lk7t7MQ5gxOi2u86ZcWtz-ghtsHk,564
+tests/commands/test_view.py,sha256=036iug8YB67ZYi_qtSU_VBBAIcJZEj_EolNDRsOaVCM,662
 tests/conftest.py,sha256=F7teEGvH3mD1zO5tqd_yEWneFrmW5U8d74-IDDSAXoI,10531
 tests/fixtures/643594.clinical.SV.vcf,sha256=e-RVC96kxwrohNmiZ7xHAHcTcnWI5-NSpOVMX2zGsXA,59626
 tests/fixtures/643594.clinical.vcf.gz,sha256=CuGqNRVLnkPDy8JM9i8JhYQZn28CDM1eGenECi2dD4E,413153
@@ -90,8 +90,8 @@ tests/vcf_tools/test_check_vcf.py,sha256=bTZQOSbhXthRDwTmcfvf4sW-DMUdlpM7bBSDsmX
 tests/vcf_tools/test_format_sv_variant.py,sha256=eeQ6XI6X2lNpsVaWecu5lfdRHrDh1XZvcz9UhL7j3qo,4375
 tests/vcf_tools/test_format_variant.py,sha256=CfgCnrS5OvuIcUOCTUGCiDRUelk3fZgT7YQAytNPvvM,4176
 tests/vcf_tools/test_vcf.py,sha256=Fc9tO1IgKFo_DCfj_GrsXGx9t_69xkWhn1ZCL7IXqLU,1563
-loqusdb-2.7.10.dist-info/LICENSE,sha256=urpFcJXw3elN9kV2fFutc-lXegjuu2lqP_GSy8_CAbs,1054
-loqusdb-2.7.10.dist-info/METADATA,sha256=gk9R2uviWXIKE3TkB40x0vTW4KLZvbL9Z-D2XoSNFqg,5270
-loqusdb-2.7.10.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-loqusdb-2.7.10.dist-info/entry_points.txt,sha256=wFoWzEFjsSgXkj9FMQA8C9ihZoJ9R1XvbGuX9hEEI6E,52
-loqusdb-2.7.10.dist-info/RECORD,,
+loqusdb-2.7.11.dist-info/LICENSE,sha256=urpFcJXw3elN9kV2fFutc-lXegjuu2lqP_GSy8_CAbs,1054
+loqusdb-2.7.11.dist-info/METADATA,sha256=Kcjp_pYPIFrSDYb5sQYxHfTJY5z1ql99WYlGQSWB0SY,5270
+loqusdb-2.7.11.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+loqusdb-2.7.11.dist-info/entry_points.txt,sha256=wFoWzEFjsSgXkj9FMQA8C9ihZoJ9R1XvbGuX9hEEI6E,52
+loqusdb-2.7.11.dist-info/RECORD,,

tests/commands/test_export.py

@@ -2,7 +2,8 @@ from click.testing import CliRunner
 
 from loqusdb.commands.cli import cli as base_command
 
-def test_export_base(real_db_name:str):
+
+def test_export_base(real_db_name: str):
     """Test the base command that exports variants."""
 
     runner = CliRunner()
@@ -13,4 +14,3 @@ def test_export_base(real_db_name:str):
     ## THEN it should return success
     result = runner.invoke(base_command, command)
     assert result.exit_code == 0
-

tests/commands/test_identity.py

@@ -2,7 +2,8 @@ from click.testing import CliRunner
 
 from loqusdb.commands.cli import cli as base_command
 
-def test_identity(real_db_name:str):
+
+def test_identity(real_db_name: str):
     """Test the SV identity base command."""
 
     runner = CliRunner()
@@ -16,7 +17,3 @@ def test_identity(real_db_name:str):
 
     # AND no variant found message
     assert "No hits for variant" in result.output
-
-
-
-

tests/commands/test_view.py

@@ -1,8 +1,10 @@
 from click.testing import CliRunner
-from loqusdb.plugins.mongo.adapter import MongoAdapter
+
 from loqusdb.commands.cli import cli as base_command
+from loqusdb.plugins.mongo.adapter import MongoAdapter
+
 
-def test_view_cases_base(real_mongo_adapter: MongoAdapter, real_db_name:str):
+def test_view_cases_base(real_mongo_adapter: MongoAdapter, real_db_name: str):
     """Test the base command that returns database cases."""
 
     ## GIVEN an empty database
@@ -11,7 +13,7 @@ def test_view_cases_base(real_mongo_adapter: MongoAdapter, real_db_name:str):
     runner = CliRunner()
 
     # THEN the case command should return No cases found error
-    command = ["--database", real_db_name, "cases" ]
+    command = ["--database", real_db_name, "cases"]
     result = runner.invoke(base_command, command)
     assert result.exit_code == 1
-    assert "No cases found in database" in result.output
+    assert "No cases found in database" in result.output