loqusdb 2.7.3__tar.gz → 2.7.8__tar.gz

{loqusdb-2.7.3 → loqusdb-2.7.8}/PKG-INFO

@@ -1,50 +1,49 @@
 Metadata-Version: 2.1
 Name: loqusdb
-Version: 2.7.3
-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-2.7.3 → 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-2.7.3 → 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-2.7.3 → 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-2.7.8/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-2.7.3 → 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-2.7.3 → 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-2.7.3 → 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-2.7.3/CHANGELOG.md

@@ -1,73 +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/)
-
-## [2.8]
-### 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
-
-## [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-2.7.3/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-2.7.3/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

loqusdb-2.7.3/loqusdb.egg-info/PKG-INFO

@@ -1,174 +0,0 @@
-Metadata-Version: 2.1
-Name: loqusdb
-Version: 2.7.3
-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
-License: MIT
-Keywords: vcf,variants
-Platform: UNKNOWN
-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
-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].
-
-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`
-
-or
-
-```
-$git clone https://github.com/moonso/loqusdb
-$cd loqusdb
-$pip install --editable .
-```
-
-## Idea ##
-
-Tool to keep track of what variants that have been seen and in what families they have been observed.
-This is **NOT** a tool to create a true frequency database.
-It will basically count the number of times we have seen a variant in any individual.
-We will also keep track of the variants that have been seen in a homozygous or hemizygous state.
-
-Variants are stored by providing a vcf file and a (ped or ped like)family file.
-
-Loqusdb will first check if the vcf file looks ok.
-
-The tool will then check all variants if they have been observed in any of the individuals in the family.
-
-When the variants are added:
-
-- Either the variant exists, in this case we increase the number of observations with one
-- Or this variant has not ben seen before, then the variant is added to database
-
-
-## Command Line Interface ##
-
-```
-$ loqusdb
-Usage: loqusdb [OPTIONS] COMMAND [ARGS]...
-
-  loqusdb: manage a local variant count database.
-
-Options:
-  -db, --database TEXT            Defaults to 'loqusdb' if not specified
-  -u, --username TEXT
-  -p, --password TEXT
-  -a, --authdb TEXT               If authentication should be done against
-                                  another database than --database
-
-  -port, --port INTEGER           Specify the port where to look for the mongo
-                                  database.  [default: 27017]
-
-  -h, --host TEXT                 Specify the host where to look for the mongo
-                                  database.  [default: localhost]
-
-  --uri TEXT                      Specify a mongodb uri
-  -c, --config FILENAME           Use a config with db information
-  -t, --test                      Used for testing. This will use a mongomock
-                                  database.
-
-  -g, --genome-build [GRCh37|GRCh38]
-                                  Specify what genome build to use
-  -v, --verbose
-  --version                       Show the version and exit.
-  --help                          Show this message and exit.
-
-Commands:
-  annotate  Annotate a VCF with observations
-  cases     Display cases in database
-  delete    Delete the variants of a family
-  dump      Dump the database
-  export    Export variants to VCF format
-  identity  Search identity collection
-  index     Add indexes to database
-  load      Load the variants of a family
-  migrate   Migrate an old loqusdb instance
-  profile   Loads variants to be used in profiling
-  restore   Restore database from dump
-  update    Update an existing case with a new type of variants
-  variants  Display variants in database
-  wipe      Wipe a loqusdb instance
-```
-
-
-## Database ##
-
-### 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:
-
-```yaml
-uri: mongodb://loqusdb-username:loqusdb-pwd@localhost:27030/loqusdb-rd?authSource=admin
-db_name: loqusdb_test
-```
-or
-```yaml
-host: localhost
-port: 27030
-username: loqusdb-username
-password: loqusdb-pwd
-authdb: admin
-db_name: loqusdb_test
-```
-
-### Mongo ###
-
-The collections looks like:
-
-**Case**
-
-```python
-{
-    'case_id': 'case_id',
-    'vcf_path': 'path_to_vcf'
-}
-```
-
-**Variant**
-
-```python
-{
-    '_id': 'variant_id',
-    'chrom': 'CHROM',
-    'start': postition,
-    'end': end postition,
-    'ref': reference base(s),
-    'alt': alternative base(s),
-    'homozygote': number_of_homozygotes,
-    'hemizygote': number_of_hemizygotes,
-    'observations': number_of_observations,
-    'families': ['family_id', ...]
-}
-```
-
-[mongodb]: https://www.mongodb.org
-[publication]: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03609-z
-[pypi-img]: https://img.shields.io/pypi/v/loqusdb.svg?style=flat-square
-[pypi-url]: https://pypi.python.org/pypi/loqusdb/
-
-

loqusdb-2.7.3/loqusdb.egg-info/SOURCES.txt

@@ -1,100 +0,0 @@
-CHANGELOG.md
-CONTRIBUTING.md
-LICENSE
-MANIFEST.in
-README.md
-setup.py
-loqusdb/__init__.py
-loqusdb/__main__.py
-loqusdb/log.py
-loqusdb.egg-info/PKG-INFO
-loqusdb.egg-info/SOURCES.txt
-loqusdb.egg-info/dependency_links.txt
-loqusdb.egg-info/entry_points.txt
-loqusdb.egg-info/requires.txt
-loqusdb.egg-info/top_level.txt
-loqusdb/build_models/__init__.py
-loqusdb/build_models/case.py
-loqusdb/build_models/profile_variant.py
-loqusdb/build_models/variant.py
-loqusdb/commands/__init__.py
-loqusdb/commands/annotate.py
-loqusdb/commands/cli.py
-loqusdb/commands/delete.py
-loqusdb/commands/export.py
-loqusdb/commands/identity.py
-loqusdb/commands/load.py
-loqusdb/commands/load_profile.py
-loqusdb/commands/migrate.py
-loqusdb/commands/restore.py
-loqusdb/commands/update.py
-loqusdb/commands/view.py
-loqusdb/commands/wipe.py
-loqusdb/constants/__init__.py
-loqusdb/exceptions/__init__.py
-loqusdb/exceptions/case.py
-loqusdb/exceptions/profile.py
-loqusdb/exceptions/vcf.py
-loqusdb/models/__init__.py
-loqusdb/models/case.py
-loqusdb/models/identity.py
-loqusdb/models/profile_variant.py
-loqusdb/models/variant.py
-loqusdb/plugins/__init__.py
-loqusdb/plugins/mongo/__init__.py
-loqusdb/plugins/mongo/adapter.py
-loqusdb/plugins/mongo/case.py
-loqusdb/plugins/mongo/profile_variant.py
-loqusdb/plugins/mongo/structural_variant.py
-loqusdb/plugins/mongo/variant.py
-loqusdb/resources/__init__.py
-loqusdb/utils/__init__.py
-loqusdb/utils/annotate.py
-loqusdb/utils/case.py
-loqusdb/utils/delete.py
-loqusdb/utils/load.py
-loqusdb/utils/migrate.py
-loqusdb/utils/profiling.py
-loqusdb/utils/update.py
-loqusdb/utils/variant.py
-loqusdb/utils/vcf.py
-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
-tests/fixtures/funny_trio.ped
-tests/fixtures/profile_snv.vcf
-tests/fixtures/recessive_trio.ped
-tests/fixtures/test.SV.vcf
-tests/fixtures/test.vcf
-tests/fixtures/test.vcf.gz
-tests/fixtures/test.vcf.gz.tbi
-tests/fixtures/unsorted.vcf
-tests/functional/test_cli.py
-tests/plugins/mongo/test_case_operations.py
-tests/plugins/mongo/test_connect.py
-tests/plugins/mongo/test_flask_extension.py
-tests/plugins/mongo/test_get_sv.py
-tests/plugins/mongo/test_load_svs.py
-tests/plugins/mongo/test_variant_operations.py
-tests/utils/test_case.py
-tests/utils/test_delete.py
-tests/utils/test_delete_family.py
-tests/utils/test_delete_variant.py
-tests/utils/test_get_family.py
-tests/utils/test_load_database.py
-tests/utils/test_load_family.py
-tests/utils/test_load_variants.py
-tests/utils/test_migrate.py
-tests/utils/test_profiling.py
-tests/vcf_tools/test_check_par.py
-tests/vcf_tools/test_check_vcf.py
-tests/vcf_tools/test_format_sv_variant.py
-tests/vcf_tools/test_format_variant.py
-tests/vcf_tools/test_vcf.py

loqusdb-2.7.3/loqusdb.egg-info/dependency_links.txt

@@ -1 +0,0 @@
-

loqusdb-2.7.3/loqusdb.egg-info/entry_points.txt

@@ -1,3 +0,0 @@
-[console_scripts]
-loqusdb = loqusdb.__main__:base_command
-

loqusdb-2.7.3/loqusdb.egg-info/requires.txt

@@ -1,13 +0,0 @@
-pytest==5.4.3
-cyvcf2==0.30.12
-mongomock
-click==7.1.2
-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
-ped_parser

loqusdb-2.7.3/loqusdb.egg-info/top_level.txt

@@ -1 +0,0 @@
-loqusdb

loqusdb-2.7.3/setup.cfg

@@ -1,4 +0,0 @@
-[egg_info]
-tag_build = 
-tag_date = 0
-

loqusdb-2.7.3/setup.py

@@ -1,83 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-# Note: To use the 'upload' functionality of this file, you must:
-#   $ pip install twine
-"""Based on https://github.com/kennethreitz/setup.py"""
-
-import io
-import os
-
-from setuptools import find_packages, setup
-
-# Package meta-data.
-NAME = "loqusdb"
-DESCRIPTION = "Store observations of vcf variants in a mongodb"
-URL = "https://github.com/moonso/loqusdb"
-EMAIL = "mans.magnusson@scilifelab.com"
-AUTHOR = "Måns Magnusson"
-REQUIRES_PYTHON = ">=3.7.0"
-VERSION = "2.7.3"
-
-with open('requirements.txt') as f:
-    install_requires = f.read().strip().split('\n')
-
-# The rest you shouldn't have to touch too much :)
-# ------------------------------------------------
-# Except, perhaps the License and Trove Classifiers!
-# If you do change the License, remember to change the Trove Classifier for that!
-
-here = os.path.abspath(os.path.dirname(__file__))
-
-# Import the README and use it as the long-description.
-# Note: this will only work if 'README.md' is present in your MANIFEST.in file!
-try:
-    with io.open(os.path.join(here, "README.md"), encoding="utf-8") as f:
-        long_description = "\n" + f.read()
-except FileNotFoundError:
-    long_description = DESCRIPTION
-
-# Load the package's __version__.py module as a dictionary.
-about = {}
-if not VERSION:
-    with open(os.path.join(here, NAME, "__version__.py")) as f:
-        exec(f.read(), about)
-else:
-    about["__version__"] = VERSION
-
-
-# Where the magic happens:
-setup(
-    name=NAME,
-    version=about["__version__"],
-    description=DESCRIPTION,
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    author=AUTHOR,
-    author_email=EMAIL,
-    python_requires=REQUIRES_PYTHON,
-    url=URL,
-    packages=find_packages(exclude=("tests",)),
-    entry_points={
-        "console_scripts": ["loqusdb = loqusdb.__main__:base_command"],
-    },
-    install_requires=install_requires,
-    include_package_data=True,
-    license="MIT",
-    keywords=["vcf", "variants"],
-    classifiers=[
-        # Trove classifiers
-        # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers
-        "License :: OSI Approved :: MIT License",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: Implementation :: CPython",
-        "Operating System :: MacOS :: MacOS X",
-        "Operating System :: Unix",
-        "Intended Audience :: Science/Research",
-        "Topic :: Scientific/Engineering :: Bio-Informatics",
-    ],
-)