loqusdb 2.7.2__tar.gz → 2.7.8__tar.gz

{loqusdb-2.7.2 → loqusdb-2.7.8}/PKG-INFO

@@ -1,50 +1,49 @@
 Metadata-Version: 2.1
 Name: loqusdb
-Version: 2.7.2
-Summary: Store observations of vcf variants in a mongodb
-Home-page: https://github.com/moonso/loqusdb
-Author: Måns Magnusson
-Author-email: mans.magnusson@scilifelab.com
+Version: 2.7.8
+Summary: A simple observation count database
 License: MIT
-Keywords: vcf,variants
-Platform: UNKNOWN
+Author: Your Name
+Author-email: you@example.com
+Requires-Python: >=3.12,<4.0
 Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: Implementation :: CPython
-Classifier: Operating System :: MacOS :: MacOS X
-Classifier: Operating System :: Unix
-Classifier: Intended Audience :: Science/Research
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Requires-Python: >=3.7.0
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: PyYAML
+Requires-Dist: click
+Requires-Dist: coloredlogs
+Requires-Dist: cyvcf2
+Requires-Dist: mongo-adapter
+Requires-Dist: numpy
+Requires-Dist: ped_parser
+Requires-Dist: pymongo
+Requires-Dist: setuptools
+Requires-Dist: vcftoolbox
 Description-Content-Type: text/markdown
-License-File: LICENSE
-
 
 # loqusdb
 [![Publish to PyPI](https://github.com/moonso/loqusdb/actions/workflows/build_and_publish.yml/badge.svg)](https://github.com/moonso/loqusdb/actions/workflows/build_and_publish.yml)
 [![Coverage Status](https://coveralls.io/repos/github/moonso/loqusdb/badge.svg?branch=master)](https://coveralls.io/github/moonso/loqusdb?branch=master)
 [![PyPI Version][pypi-img]][pypi-url]
 
-Small tool to setup a local variant database. If you find loqusdb useful in your work, please cite the [article][publication].
+Small tool to set up a local variant database.
+If you find Loqusdb useful in your work, please cite the [article][publication].
 
-Right now **locusdb** uses [mongodb][mongodb] as backend for
-storing variants but there should not be a huge difference to use another
+Right now **Locusdb** uses [mongodb][mongodb] as backend for
+storing variants, but there should not be a huge difference to use another
 database manager.
 
 ## Installation ##
 
-These instructions were written and tested using a conda environment with a version of **Python >=3.9**, which is required by the installer file (setup.py).
 
-`pip install loqusdb`
+`poetry install`
 
 or
 
 ```
 $git clone https://github.com/moonso/loqusdb
 $cd loqusdb
-$pip install --editable .
+$poetry install
 ```
 
 ## Idea ##
@@ -54,16 +53,16 @@ This is **NOT** a tool to create a true frequency database.
 It will basically count the number of times we have seen a variant in any individual.
 We will also keep track of the variants that have been seen in a homozygous or hemizygous state.
 
-Variants are stored by providing a vcf file and a (ped or ped like)family file.
+Variants are stored by providing a VCF file and a (ped or ped like) family file.
 
-Loqusdb will first check if the vcf file looks ok.
+Loqusdb will first check if the VCF file adheres to the VCF format.
 
 The tool will then check all variants if they have been observed in any of the individuals in the family.
 
 When the variants are added:
 
 - Either the variant exists, in this case we increase the number of observations with one
-- Or this variant has not ben seen before, then the variant is added to database
+- Or this variant has not been seen before, then the variant is added to the database
 
 
 ## Command Line Interface ##
@@ -120,7 +119,7 @@ Commands:
 
 ### Connecting ###
 
-Connection can be specified on command line with `--database`, `--username`, `--password`, `--port`, `--host` and/or `--uri`. Or these options can be sent with a config file that can take the same options, looks like:
+Connection can be specified on command line with `--database`, `--username`, `--password`, `--port`, `--host` and/or `--uri`. Or these options can be sent with a config file that can take the same options:
 
 ```yaml
 uri: mongodb://loqusdb-username:loqusdb-pwd@localhost:27030/loqusdb-rd?authSource=admin
@@ -138,7 +137,7 @@ db_name: loqusdb_test
 
 ### Mongo ###
 
-The collections looks like:
+The collections are defined as follows:
 
 **Case**
 
@@ -171,4 +170,3 @@ The collections looks like:
 [pypi-img]: https://img.shields.io/pypi/v/loqusdb.svg?style=flat-square
 [pypi-url]: https://pypi.python.org/pypi/loqusdb/
 
-

{loqusdb-2.7.2 → loqusdb-2.7.8}/README.md

@@ -3,24 +3,24 @@
 [![Coverage Status](https://coveralls.io/repos/github/moonso/loqusdb/badge.svg?branch=master)](https://coveralls.io/github/moonso/loqusdb?branch=master)
 [![PyPI Version][pypi-img]][pypi-url]
 
-Small tool to setup a local variant database. If you find loqusdb useful in your work, please cite the [article][publication].
+Small tool to set up a local variant database.
+If you find Loqusdb useful in your work, please cite the [article][publication].
 
-Right now **locusdb** uses [mongodb][mongodb] as backend for
-storing variants but there should not be a huge difference to use another
+Right now **Locusdb** uses [mongodb][mongodb] as backend for
+storing variants, but there should not be a huge difference to use another
 database manager.
 
 ## Installation ##
 
-These instructions were written and tested using a conda environment with a version of **Python >=3.9**, which is required by the installer file (setup.py).
 
-`pip install loqusdb`
+`poetry install`
 
 or
 
 ```
 $git clone https://github.com/moonso/loqusdb
 $cd loqusdb
-$pip install --editable .
+$poetry install
 ```
 
 ## Idea ##
@@ -30,16 +30,16 @@ This is **NOT** a tool to create a true frequency database.
 It will basically count the number of times we have seen a variant in any individual.
 We will also keep track of the variants that have been seen in a homozygous or hemizygous state.
 
-Variants are stored by providing a vcf file and a (ped or ped like)family file.
+Variants are stored by providing a VCF file and a (ped or ped like) family file.
 
-Loqusdb will first check if the vcf file looks ok.
+Loqusdb will first check if the VCF file adheres to the VCF format.
 
 The tool will then check all variants if they have been observed in any of the individuals in the family.
 
 When the variants are added:
 
 - Either the variant exists, in this case we increase the number of observations with one
-- Or this variant has not ben seen before, then the variant is added to database
+- Or this variant has not been seen before, then the variant is added to the database
 
 
 ## Command Line Interface ##
@@ -96,7 +96,7 @@ Commands:
 
 ### Connecting ###
 
-Connection can be specified on command line with `--database`, `--username`, `--password`, `--port`, `--host` and/or `--uri`. Or these options can be sent with a config file that can take the same options, looks like:
+Connection can be specified on command line with `--database`, `--username`, `--password`, `--port`, `--host` and/or `--uri`. Or these options can be sent with a config file that can take the same options:
 
 ```yaml
 uri: mongodb://loqusdb-username:loqusdb-pwd@localhost:27030/loqusdb-rd?authSource=admin
@@ -114,7 +114,7 @@ db_name: loqusdb_test
 
 ### Mongo ###
 
-The collections looks like:
+The collections are defined as follows:
 
 **Case**
 

{loqusdb-2.7.2 → loqusdb-2.7.8}/loqusdb/__init__.py

@@ -1,11 +1,10 @@
 import logging
 
-from pkg_resources import get_distribution
 from pymongo import ASCENDING, IndexModel
 
 logger = logging.getLogger(__name__)
 
-__version__ = get_distribution("loqusdb").version
+__version__ = "2.7.7"
 
 INDEXES = {
     "variant": [
@@ -28,12 +27,14 @@ INDEXES = {
     "structural_variant": [
         IndexModel(
             [
+                ("sv_type", ASCENDING),
                 ("chrom", ASCENDING),
                 ("end_chrom", ASCENDING),
-                ("sv_type", ASCENDING),
                 ("pos_left", ASCENDING),
+                ("pos_right", ASCENDING),
             ],
             name="coordinates",
+            background=True,
         ),
         IndexModel(
             [
@@ -42,6 +43,7 @@ INDEXES = {
                 ("end_right", ASCENDING),
             ],
             name="short_coordinates",
+            background=True,
         ),
     ],
     "identity": [

{loqusdb-2.7.2 → loqusdb-2.7.8}/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-2.7.8}/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-2.7.8}/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-2.7.8}/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-2.7.8}/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-2.7.8/pyproject.toml

@@ -0,0 +1,38 @@
+[tool.poetry]
+name = "loqusdb"
+version = "2.7.8"
+description = "A simple observation count database"
+authors = ["Your Name <you@example.com>"]
+license = "MIT"
+readme = "README.md"
+include = [
+  "README.md",
+  "loqusdb/**/*",
+  "tests/**/*"
+]
+
+[tool.poetry.dependencies]
+python = "^3.12"
+cyvcf2 = "*"
+click = "*"
+pymongo = "*"
+numpy = "*"
+coloredlogs = "*"
+PyYAML = "*"
+vcftoolbox = "*"
+setuptools = "*"
+mongo-adapter = "*"
+ped_parser = "*"
+
+[tool.poetry.group.dev.dependencies]
+coveralls =  "^3"
+mongomock = "*"
+pytest = "*"
+pytest-cov = "*"
+
+[tool.poetry.scripts]
+loqusdb = "loqusdb.commands.cli:cli"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

loqusdb-2.7.8/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-2.7.8/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-2.7.8/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-2.7.8}/tests/conftest.py

@@ -65,14 +65,14 @@ def real_db_name(request):
 @pytest.fixture(scope="function")
 def mongo_client(request):
     """Return a mongomock client"""
-    client = MockClient()
+    client = MockClient(directConnection=True)
     return client
 
 
 @pytest.fixture(scope="function")
 def real_mongo_client(request):
     """Return a mongomock client"""
-    client = MongoClient()
+    client = MongoClient(directConnection=True)
 
     def teardown():
         print("\n")

{loqusdb-2.7.2 → loqusdb-2.7.8}/tests/fixtures/profile_snv.vcf

@@ -25,7 +25,7 @@
 ##contig=<ID=Y,length=59373566>
 ##contig=<ID=MT,length=16569>
 ##reference=file:///humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT  proband_2
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	proband_2
 1	44072018	rs1065772	C	T	.	.	CAF=[0.7121,0.2879];COMMON=1;G5;GNO;HD;KGPROD;KGPhase1;OTHERKG;PH3;REF;RS=1065772;RSPOS=44072018;SAO=0;SLO;SSR=0;SYN;VC=SNV;VLD;VP=0x050100000301150517000100;WGT=1;dbSNPBuildID=86 GT  ./.
 1	183072590	rs2296288	T	C	.	.	CAF=[0.4656,0.5344];COMMON=1;G5;G5A;GNO;HD;KGPROD;KGPhase1;KGPilot123;OTHERKG;PH3;REF;RS=2296288;RSPOS=183072590;SAO=0;SLO;SSR=0;SYN;VC=SNV;VLD;VP=0x05010000030117051f000100;WGT=1;dbSNPBuildID=100 GT  ./.
 1	212619339	rs4804	T	C	.	.	CAF=[0.5069,0.4931];COMMON=1;G5;G5A;GNO;HD;KGPROD;KGPhase1;KGPilot123;OTHERKG;PH3;REF;RS=4804;RSPOS=212619339;SAO=0;SLO;SSR=0;SYN;VC=SNV;VLD;VP=0x05010000030117051f000101;WGT=1;dbSNPBuildID=52 GT  ./.

{loqusdb-2.7.2 → loqusdb-2.7.8}/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

loqusdb-2.7.2/CHANGELOG.md

@@ -1,66 +0,0 @@
-# Change Log
-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/)
-
-## [unreleased]
-### Fixed
-- `Deprecated config in setup.cfg` error when installing the package
-
-## [2.7.1]
-### Added
-- Script to correct contig name
-- Expanded instructions on how to set up an instance and load data into database
-### Changed
-- GitHub actions run tests using MongoDB versions 3.2, 4.4 and 5.0
-### Fixed
-- Restore command accepts custom database name
-- Restore command uses either database URI or host:port params
-
-## [2.5.2]
-
-### Changed
-- Convert version to string
-- Use Github Actions for running CI instead of Travis
-
-## [2.5.1]
-
-### Added
-- Option to add observation frequencies to exported VCF (--freq)
-
-## [2.5]
-
-### Added
-- Profiling feature added. Each sample gets a profile based on the genotypes for
-a set of high maf variants.
-- High maf variants used in profiling is loaded into DB via CLI
-- Reject loading a case if a similar profile already exists for any of the samples
-- Statistics of the profiles in DB can be generated through CLI
-- use bulk operations when deleting variants
-- Compatible with GRCh38
-- Option to include case count when querying for a variant
-
-### Fixed
-- Use correct fields in index
-
-## [2.3]
-
-### Added
-- Use bulk updates when inserting snvs
-
-## [2.2]
-
-### Added
-- CLI function to annotate variants
-- CLI functionality to dump and restore a database
-
-## [2.1]
-
-### Fixed
-- Fix bug with inserting variants
-
-### [2.0]
-
-### Added
-- Adds structural variants to loqus

loqusdb-2.7.2/CONTRIBUTING.md

@@ -1,5 +0,0 @@
-## Versioning
-LoqusDB adheres to [semantic versioning](https://semver.org/).
-
-## Branching model
-LoqusDB follows a githubflow [branching model](https://guides.github.com/introduction/flow/).

loqusdb-2.7.2/MANIFEST.in

@@ -1,10 +0,0 @@
-include AUTHORS
-include CONTRIBUTING.md
-include CHANGELOG.md
-include LICENSE
-include README.md
-
-recursive-include tests *
-recursive-exclude * __pycache__
-recursive-exclude * *.py[co]
-recursive-exclude * *.db