loqusdb 2.7.10__py3-none-any.whl → 2.7.12__py3-none-any.whl

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/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/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/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/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/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.

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/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.dist-info → loqusdb-2.7.12.dist-info}/METADATA

@@ -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-2.7.12.dist-info/RECORD

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{loqusdb-2.7.10.dist-info → loqusdb-2.7.12.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.0
+Generator: poetry-core 2.0.0
 Root-Is-Purelib: true
 Tag: py3-none-any

README.md

@@ -1,148 +0,0 @@
-# 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-2.7.10.dist-info/RECORD

@@ -1,97 +0,0 @@
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