loqusdb 2.7.2__tar.gz → 2.7.4__tar.gz

{loqusdb-2.7.2 → loqusdb-2.7.4}/CHANGELOG.md

@@ -3,8 +3,18 @@ All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
 About changelog [here](https://keepachangelog.com/en/1.0.0/)
+## [2.7.4]
+## Changed
+- When using QUAL values, treat . as 0 quality
 
-## [unreleased]
+## [2.7.3]
+### Added
+- Basic cli tests touching fixed deprecated code
+### Changed
+- Unfreezed PyMongo in requirements.txt
+- Replaced deprecated pymongo `.count()` function with `count_documents()` in code.
+
+## [2.7.2]
 ### Fixed
 - `Deprecated config in setup.cfg` error when installing the package
 

{loqusdb-2.7.2 → loqusdb-2.7.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: loqusdb
-Version: 2.7.2
+Version: 2.7.4
 Summary: Store observations of vcf variants in a mongodb
 Home-page: https://github.com/moonso/loqusdb
 Author: Måns Magnusson

{loqusdb-2.7.2 → loqusdb-2.7.4}/loqusdb/build_models/variant.py

@@ -1,8 +1,12 @@
 import logging
 from collections import namedtuple
 
+import cyvcf2
+
+from typing import Optional
+
 from loqusdb.constants import CHROM_TO_INT, GENOTYPE_MAP, GRCH37, PAR
-from loqusdb.models import Variant
+from loqusdb.models import Case, Variant
 
 LOG = logging.getLogger(__name__)
 
@@ -139,19 +143,21 @@ def get_coords(variant):
     return coordinates
 
 
-def build_variant(variant, case_obj, case_id=None, gq_threshold=None, gq_qual=False, genome_build=None):
+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.
 
-    If criterias are not fullfilled, eg. variant have no gt call or quality
+    If criteria are not fulfilled, eg variant has no GT call or quality.
     is below gq threshold then return None.
 
+
     Args:
         variant(cyvcf2.Variant)
         case_obj(Case): We need the case object to check individuals sex
         case_id(str): The case id
         gq_threshold(int): Genotype Quality threshold
+        gq_qual(bool): Use variant.QUAL for quality instead of GQ
 
     Return:
         formated_variant(models.Variant): A variant dictionary
@@ -190,7 +196,9 @@ def build_variant(variant, case_obj, case_id=None, gq_threshold=None, gq_qual=Fa
             ind_pos = ind_obj["ind_index"]
 
             if gq_qual:
-                gq = int(variant.QUAL)
+                gq = 0
+                if variant.QUAL:
+                    gq = int(variant.QUAL)
 
             if not gq_qual:
                 gq = int(variant.gt_quals[ind_pos])

{loqusdb-2.7.2 → loqusdb-2.7.4}/loqusdb/commands/export.py

@@ -39,7 +39,6 @@ def export(ctx, outfile, variant_type, freq):
     version = ctx.obj["version"]
 
     LOG.info("Export the variants from {0}".format(adapter))
-    nr_cases = 0
 
     is_sv = variant_type == "sv"
     existing_chromosomes = set(adapter.get_chromosomes(sv=is_sv))
@@ -52,8 +51,8 @@ def export(ctx, outfile, variant_type, freq):
     for chrom in existing_chromosomes:
         ordered_chromosomes.append(chrom)
 
-    nr_cases = adapter.cases().count()
-    LOG.info("Found {0} cases in database".format(nr_cases))
+    nr_cases = adapter.case_count()
+    LOG.info(f"Found {nr_cases} cases in database")
 
     head = HeaderParser()
     head.add_fileformat("VCFv4.3")
@@ -85,7 +84,7 @@ def export(ctx, outfile, variant_type, freq):
         else:
             LOG.info("Collecting all SV variants")
             variants = adapter.get_sv_variants(chromosome=chrom)
-        LOG.info("{} variants found".format(variants.count()))
+        LOG.info(f"{adapter.nr_variants(chromosome=chrom)} variants found")
         for variant in variants:
             variant_line = format_variant(
                 variant, variant_type=variant_type, nr_cases=nr_cases, add_freq=freq

{loqusdb-2.7.2 → loqusdb-2.7.4}/loqusdb/commands/identity.py

@@ -17,13 +17,12 @@ def identity(ctx, variant_id):
         ctx.abort()
 
     adapter = ctx.obj["adapter"]
-    version = ctx.obj["version"]
 
     LOG.info("Search variants {0}".format(adapter))
 
-    result = adapter.get_clusters(variant_id)
-    if result.count() == 0:
-        LOG.info("No hits for variant %s", variant_id)
+    variant_count: int = adapter.db.identity.count_documents({"variant_id": variant_id})
+    if variant_count == 0:
+        LOG.info(f"No hits for variant {variant_id}")
         return
 
     for res in result:

{loqusdb-2.7.2 → loqusdb-2.7.4}/loqusdb/commands/view.py

@@ -2,6 +2,7 @@
 import json
 import logging
 from pprint import pprint as pp
+from pymongo.cursor import Cursor
 
 import click
 
@@ -42,10 +43,12 @@ def cases(ctx, case_id, to_json, count, case_type):
         case_obj["_id"] = str(case_obj["_id"])
         cases.append(case_obj)
     else:
-        cases = adapter.cases()
-        if cases.count() == 0:
+        case_count: int = adapter.case_count()
+        if case_count == 0:
             LOG.info("No cases found in database")
             ctx.abort()
+        cases: Cursor = adapter.cases()
+
 
     if to_json:
         click.echo(json.dumps(cases))

{loqusdb-2.7.2 → loqusdb-2.7.4}/loqusdb/plugins/mongo/case.py

@@ -99,13 +99,6 @@ class CaseMixin:
         LOG.info("Removing case {0} from database".format(mongo_case.get("case_id")))
         self.db.case.delete_one({"_id": mongo_case["_id"]})
 
-    def case_count(self):
-        """Returns the total number of cases in the database
-
-        returns:
-            nr_of_cases (int): Total number of cases in database
-        """
-        nr_of_cases = 0
-        res = self.cases
-
-        return res.count()
+    def case_count(self) -> int:
+        """Returns the total number of cases in the database."""
+        return self.db.case.count_documents({})

{loqusdb-2.7.2 → loqusdb-2.7.4}/loqusdb.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: loqusdb
-Version: 2.7.2
+Version: 2.7.4
 Summary: Store observations of vcf variants in a mongodb
 Home-page: https://github.com/moonso/loqusdb
 Author: Måns Magnusson

{loqusdb-2.7.2 → loqusdb-2.7.4}/loqusdb.egg-info/SOURCES.txt

@@ -62,6 +62,9 @@ tests/conftest.py
 tests/build_models/test_build_case.py
 tests/build_models/test_build_variant.py
 tests/build_models/test_is_greater.py
+tests/commands/test_export.py
+tests/commands/test_identity.py
+tests/commands/test_view.py
 tests/fixtures/643594.clinical.SV.vcf
 tests/fixtures/643594.clinical.vcf.gz
 tests/fixtures/double_variant.vcf

{loqusdb-2.7.2 → loqusdb-2.7.4}/loqusdb.egg-info/requires.txt

@@ -1,13 +1,13 @@
 pytest==5.4.3
 cyvcf2==0.30.12
-mongomock==3.18.0
+mongomock
 click==7.1.2
-pymongo==3.7.1
+pymongo
 numpy==1.21.4
 coloredlogs==14.0
 pyyaml>=5.4.1
 vcftoolbox==1.5
 pip==23.1.2
 setuptools==65.5.1
-mongo_adapter>=0.3.3
+mongo_adapter
 ped_parser

{loqusdb-2.7.2 → loqusdb-2.7.4}/setup.py

@@ -19,7 +19,7 @@ URL = "https://github.com/moonso/loqusdb"
 EMAIL = "mans.magnusson@scilifelab.com"
 AUTHOR = "Måns Magnusson"
 REQUIRES_PYTHON = ">=3.7.0"
-VERSION = "2.7.2"
+VERSION = "2.7.4"
 
 with open('requirements.txt') as f:
     install_requires = f.read().strip().split('\n')

loqusdb-2.7.4/tests/commands/test_export.py

@@ -0,0 +1,16 @@
+from click.testing import CliRunner
+
+from loqusdb.commands.cli import cli as base_command
+
+def test_export_base(real_db_name:str):
+    """Test the base command that exports variants."""
+
+    runner = CliRunner()
+
+    # WHEN the base command to export cases is run
+    command = ["--database", real_db_name, "export"]
+
+    ## THEN it should return success
+    result = runner.invoke(base_command, command)
+    assert result.exit_code == 0
+

loqusdb-2.7.4/tests/commands/test_identity.py

@@ -0,0 +1,22 @@
+from click.testing import CliRunner
+
+from loqusdb.commands.cli import cli as base_command
+
+def test_identity(real_db_name:str):
+    """Test the SV identity base command."""
+
+    runner = CliRunner()
+
+    # WHEN the base identity command is run on an empty database
+    command = ["--database", real_db_name, "identity", "-v", "1_7890024_TGA_GGG"]
+
+    # THEN the command should return success
+    result = runner.invoke(base_command, command)
+    assert result.exit_code == 0
+
+    # AND no variant found message
+    assert "No hits for variant" in result.output
+
+
+
+

loqusdb-2.7.4/tests/commands/test_view.py

@@ -0,0 +1,17 @@
+from click.testing import CliRunner
+from loqusdb.plugins.mongo.adapter import MongoAdapter
+from loqusdb.commands.cli import cli as base_command
+
+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
+    assert sum([1 for _ in real_mongo_adapter.cases()]) == 0
+
+    runner = CliRunner()
+
+    # THEN the case command should return No cases found error
+    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

{loqusdb-2.7.2 → loqusdb-2.7.4}/tests/vcf_tools/test_format_variant.py

@@ -21,6 +21,20 @@ def test_format_variant(het_variant, case_obj):
     assert formated_variant["homozygote"] == 0
 
 
+def test_format_variant_no_qual(variant_no_gq, case_obj):
+    ## GIVEN a variant without GQ
+    variant = variant_no_gq
+    ## And that has a missing QUAL value
+    variant.QUAL = None
+    case_id = case_obj["case_id"]
+    ## WHEN parsing the variant using a QUAL threshold
+    formated_variant = build_variant(
+        variant=variant, case_obj=case_obj, case_id=case_id, gq_qual=True, gq_threshold=20
+    )
+    ## THEN assert that None is returned since requirements are not fulfilled
+    assert formated_variant is None
+
+
 def test_format_variant_no_gq(variant_no_gq, case_obj):
     ## GIVEN a variant without GQ
     variant = variant_no_gq