loqusdb 2.7.10__tar.gz → 2.7.12__tar.gz

{loqusdb-2.7.10 → loqusdb-2.7.12}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: loqusdb
-Version: 2.7.10
+Version: 2.7.12
 Summary: A simple observation count database
 License: MIT
 Author: Your Name
@@ -9,6 +9,7 @@ Requires-Python: >=3.12,<4.0
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: PyYAML
 Requires-Dist: click
 Requires-Dist: coloredlogs

{loqusdb-2.7.10 → loqusdb-2.7.12}/loqusdb/__init__.py

@@ -4,7 +4,7 @@ from pymongo import ASCENDING, IndexModel
 
 logger = logging.getLogger(__name__)
 
-__version__ = "2.7.10"
+__version__ = "2.7.12"
 
 INDEXES = {
     "variant": [

{loqusdb-2.7.10 → loqusdb-2.7.12}/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-2.7.10 → loqusdb-2.7.12}/loqusdb/commands/export.py

@@ -59,7 +59,10 @@ def export(ctx, outfile, variant_type, freq):
     head.add_meta_line("NrCases", nr_cases)
     if freq:
         head.add_info(
-            "Frq", "1", "Float", "Observation frequency of the variant (not allele frequency)"
+            "Frq",
+            "1",
+            "Float",
+            f"Observation frequency of the variant (not allele frequency) based on {nr_cases} cases",
         )
     head.add_info("Obs", "1", "Integer", "The number of observations for the variant")
     head.add_info("Hom", "1", "Integer", "The number of observed homozygotes")

{loqusdb-2.7.10 → loqusdb-2.7.12}/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-2.7.10 → loqusdb-2.7.12}/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-2.7.10 → loqusdb-2.7.12}/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-2.7.10 → loqusdb-2.7.12}/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 → loqusdb-2.7.12}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "loqusdb"
-version = "2.7.10"
+version = "2.7.12"
 description = "A simple observation count database"
 authors = ["Your Name <you@example.com>"]
 license = "MIT"
@@ -27,6 +27,7 @@ ped_parser = "*"
 [tool.poetry.group.dev.dependencies]
 coveralls =  "^3"
 mongomock = "*"
+pre-commit = "*"
 pytest = "*"
 pytest-cov = "*"
 
@@ -36,3 +37,14 @@ loqusdb = "loqusdb.commands.cli:cli"
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.black]
+line-length = 100
+
+[tool.isort]
+profile = "black"
+
+[tool.ruff]
+line-length = 100
+target-version = "py312"
+ignore = ["E501"]

{loqusdb-2.7.10 → loqusdb-2.7.12}/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
-

{loqusdb-2.7.10 → loqusdb-2.7.12}/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
-
-
-
-

{loqusdb-2.7.10 → loqusdb-2.7.12}/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

{loqusdb-2.7.10 → loqusdb-2.7.12}/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.