loqusdb 2.7.3__tar.gz → 2.7.6__tar.gz

{loqusdb-2.7.3 → loqusdb-2.7.6}/CHANGELOG.md

@@ -3,8 +3,11 @@ 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
 
-## [2.8]
+## [2.7.3]
 ### Added
 - Basic cli tests touching fixed deprecated code
 ### Changed

{loqusdb-2.7.3 → loqusdb-2.7.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: loqusdb
-Version: 2.7.3
+Version: 2.7.6
 Summary: Store observations of vcf variants in a mongodb
 Home-page: https://github.com/moonso/loqusdb
 Author: Måns Magnusson

{loqusdb-2.7.3 → loqusdb-2.7.6}/loqusdb/__init__.py

@@ -28,12 +28,14 @@ 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 +44,7 @@ INDEXES = {
                 ("end_right", ASCENDING),
             ],
             name="short_coordinates",
+            background=True,
         ),
     ],
     "identity": [

{loqusdb-2.7.3 → loqusdb-2.7.6}/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 → loqusdb-2.7.6}/loqusdb.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: loqusdb
-Version: 2.7.3
+Version: 2.7.6
 Summary: Store observations of vcf variants in a mongodb
 Home-page: https://github.com/moonso/loqusdb
 Author: Måns Magnusson

{loqusdb-2.7.3 → loqusdb-2.7.6}/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 = "2.7.3"
+VERSION = "2.7.6"
 
 with open('requirements.txt') as f:
     install_requires = f.read().strip().split('\n')

{loqusdb-2.7.3 → loqusdb-2.7.6}/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