loqusdb 2.7.3__py3-none-any.whl → 2.7.9__py3-none-any.whl

README.md

@@ -0,0 +1,148 @@
+# 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 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
+database manager.
+
+## Installation ##
+
+
+`poetry install`
+
+or
+
+```
+$git clone https://github.com/moonso/loqusdb
+$cd loqusdb
+$poetry install
+```
+
+## Idea ##
+
+Tool to keep track of what variants that have been seen and in what families they have been observed.
+This is **NOT** a tool to create a true frequency database.
+It will basically count the number of times we have seen a variant in any individual.
+We will also keep track of the variants that have been seen in a homozygous or hemizygous state.
+
+Variants are stored by providing a VCF file and a (ped or ped like) family file.
+
+Loqusdb will first check if the VCF file adheres to the VCF format.
+
+The tool will then check all variants if they have been observed in any of the individuals in the family.
+
+When the variants are added:
+
+- Either the variant exists, in this case we increase the number of observations with one
+- Or this variant has not been seen before, then the variant is added to the database
+
+
+## Command Line Interface ##
+
+```
+$ 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:
+
+```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 are defined as follows:
+
+**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/__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__ = "2.7.9"
 
 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/build_models/case.py

@@ -6,15 +6,8 @@ from loqusdb.models import Case, Individual
 LOG = logging.getLogger(__name__)
 
 
-def get_individual_positions(individuals):
-    """Return a dictionary with individual positions
-
-    Args:
-        individuals(list): A list with vcf individuals in correct order
-
-    Returns:
-        ind_pos(dict): Map from ind_id -> index position
-    """
+def get_individual_positions(individuals: list[str]) -> dict[str, int]:
+    """Return a dictionary with individual positions."""
     ind_pos = {}
     if individuals:
         for i, ind in enumerate(individuals):
@@ -35,7 +28,7 @@ def build_case(
     matches=None,
     profile_path=None,
 ):
-    """Build a Case from the given information
+    """Build a Case from the given information.
 
     Args:
         case(ped_parser.Family): A family object

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-2.7.3.dist-info → loqusdb-2.7.9.dist-info}/METADATA

@@ -1,63 +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: 2.7.9
+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
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: pytest ==5.4.3
-Requires-Dist: cyvcf2 ==0.30.12
-Requires-Dist: mongomock
-Requires-Dist: click ==7.1.2
-Requires-Dist: pymongo
-Requires-Dist: numpy ==1.21.4
-Requires-Dist: coloredlogs ==14.0
-Requires-Dist: pyyaml >=5.4.1
-Requires-Dist: vcftoolbox ==1.5
-Requires-Dist: pip ==23.1.2
-Requires-Dist: setuptools ==65.5.1
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: PyYAML
+Requires-Dist: click
+Requires-Dist: coloredlogs
+Requires-Dist: cyvcf2
 Requires-Dist: mongo-adapter
-Requires-Dist: ped-parser
-
+Requires-Dist: numpy
+Requires-Dist: ped_parser
+Requires-Dist: pymongo
+Requires-Dist: setuptools
+Requires-Dist: vcftoolbox
+Description-Content-Type: text/markdown
 
 # 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 ##
@@ -67,16 +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 ##
@@ -133,7 +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
@@ -151,7 +137,7 @@ db_name: loqusdb_test
 
 ### Mongo ###
 
-The collections looks like:
+The collections are defined as follows:
 
 **Case**
 
@@ -184,4 +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-2.7.9.dist-info/RECORD

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+loqusdb-2.7.9.dist-info/RECORD,,

{loqusdb-2.7.3.dist-info → loqusdb-2.7.9.dist-info}/WHEEL

@@ -1,5 +1,4 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.2)
+Generator: poetry-core 1.9.0
 Root-Is-Purelib: true
 Tag: py3-none-any
-

loqusdb-2.7.9.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+loqusdb=loqusdb.commands.cli:cli
+

tests/build_models/test_build_case.py

@@ -0,0 +1,150 @@
+import pytest
+
+from loqusdb.build_models.case import build_case, get_individual_positions
+from loqusdb.exceptions import CaseError
+
+
+def test_get_individual_positions():
+    ## GIVEN a list with ids
+    inds = ["1", "2", "3"]
+    ## WHEN getting the individual positions
+    ind_pos = get_individual_positions(inds)
+    ## THEN assert they where given the correct position
+    assert ind_pos["1"] == 0
+    assert ind_pos["2"] == 1
+    assert ind_pos["3"] == 2
+
+
+def test_get_individual_positions_no_inds():
+    ## GIVEN a list with ids
+    inds = None
+    ## WHEN getting the individual positions
+    ind_pos = get_individual_positions(inds)
+    ## THEN assert an empty dict is returned
+    assert ind_pos == {}
+
+
+def test_build_case_no_ped():
+    ## GIVEN some vcf individuals
+
+    vcf_individuals = ["mother", "proband"]
+    case_id = "test"
+
+    ## WHEN building a case object
+    case_obj = build_case(
+        case=None,
+        vcf_individuals=vcf_individuals,
+        case_id=case_id,
+    )
+
+    ## THEN assert that the case got the right ID
+    assert case_obj["case_id"] == case_id
+    for ind_obj in case_obj["individuals"]:
+        assert ind_obj["name"] in vcf_individuals
+        assert ind_obj["ind_id"] in vcf_individuals
+
+
+def test_build_case_no_ped_no_case_id():
+    ## WHEN building a case object
+
+    ## THEN assert a CaseError is raised
+    with pytest.raises(CaseError):
+        ## GIVEN some vcf individuals
+
+        vcf_individuals = ["mother", "proband"]
+
+        case_obj = build_case(
+            case=None,
+            vcf_individuals=vcf_individuals,
+        )
+
+
+def test_build_case_ped(family_obj, vcf_path):
+    ## GIVEN a ped parser family_obj
+    vcf_inds = [ind_id for ind_id in family_obj.individuals]
+    nr_variants = 10
+
+    ## WHEN building a case object
+    case_obj = build_case(
+        case=family_obj,
+        vcf_individuals=vcf_inds,
+        vcf_path=vcf_path,
+        nr_variants=nr_variants,
+    )
+
+    ## THEN assert that the case has the correct id
+    assert case_obj["case_id"] == family_obj.family_id
+
+    for ind_obj in case_obj["individuals"]:
+        assert ind_obj["ind_id"] in vcf_inds
+
+    ## THEN assert that the vcf_path was added
+    assert case_obj["vcf_path"] == vcf_path
+
+    ## THEN assert that the nr variants is correct
+    assert case_obj["nr_variants"] == nr_variants
+
+
+def test_build_case_ped_sv(family_obj, sv_vcf_path):
+    ## GIVEN a ped parser family_obj
+    vcf_inds = [ind_id for ind_id in family_obj.individuals]
+    nr_sv_variants = 10
+
+    ## WHEN building a case object
+    case_obj = build_case(
+        case=family_obj,
+        sv_individuals=vcf_inds,
+        vcf_sv_path=sv_vcf_path,
+        nr_sv_variants=nr_sv_variants,
+    )
+
+    ## THEN assert that the case has the correct id
+    assert case_obj["case_id"] == family_obj.family_id
+
+    case_obj["individuals"] == []
+    for ind_obj in case_obj["sv_individuals"]:
+        assert ind_obj["ind_id"] in vcf_inds
+
+    ## THEN assert that the vcf_path was added
+    assert case_obj["vcf_path"] is None
+    assert case_obj["vcf_sv_path"] == sv_vcf_path
+
+    ## THEN assert that the nr variants is correct
+    assert case_obj["nr_variants"] is None
+    assert case_obj["nr_sv_variants"] == nr_sv_variants
+
+
+def test_build_case_ped_sv_and_snv(family_obj, sv_vcf_path, vcf_path):
+    ## GIVEN a ped parser family_obj
+    vcf_inds = [ind_id for ind_id in family_obj.individuals]
+    sv_vcf_inds = [ind_id for ind_id in family_obj.individuals]
+    nr_sv_variants = 10
+    nr_variants = 20
+
+    ## WHEN building a case object
+    case_obj = build_case(
+        case=family_obj,
+        sv_individuals=vcf_inds,
+        vcf_sv_path=sv_vcf_path,
+        nr_sv_variants=nr_sv_variants,
+        vcf_individuals=vcf_inds,
+        vcf_path=vcf_path,
+        nr_variants=nr_variants,
+    )
+
+    ## THEN assert that the case has the correct id
+    assert case_obj["case_id"] == family_obj.family_id
+
+    for ind_obj in case_obj["individuals"]:
+        assert ind_obj["ind_id"] in vcf_inds
+
+    for ind_obj in case_obj["sv_individuals"]:
+        assert ind_obj["ind_id"] in sv_vcf_inds
+
+    ## THEN assert that the vcf_path was added
+    assert case_obj["vcf_path"] == vcf_path
+    assert case_obj["vcf_sv_path"] == sv_vcf_path
+
+    ## THEN assert that the nr variants is correct
+    assert case_obj["nr_variants"] == nr_variants
+    assert case_obj["nr_sv_variants"] == nr_sv_variants

tests/build_models/test_build_variant.py

@@ -0,0 +1,15 @@
+from loqusdb.build_models.variant import get_coords, build_variant
+
+
+def test_build_het_variant(het_variant, case_obj):
+    variant_obj = build_variant(variant=het_variant, case_obj=case_obj)
+    assert variant_obj["chrom"] == het_variant.CHROM
+    assert variant_obj["homozygote"] == 0
+    assert variant_obj["hemizygote"] == 0
+
+
+def test_get_coords_for_BND(bnd_variant):
+    coords = get_coords(bnd_variant)
+    assert coords["pos"] == coords["end"]
+    assert coords["sv_length"] == float("inf")
+    assert coords["sv_type"] == "BND"