loqusdb 2.7.3__py3-none-any.whl → 2.7.4__py3-none-any.whl

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-2.7.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: loqusdb
-Version: 2.7.3
+Version: 2.7.4
 Summary: Store observations of vcf variants in a mongodb
 Home-page: https://github.com/moonso/loqusdb
 Author: Måns Magnusson

{loqusdb-2.7.3.dist-info → loqusdb-2.7.4.dist-info}/RECORD

@@ -4,7 +4,7 @@ loqusdb/log.py,sha256=CDcrCjzs9ef-d5Wg8Q_41bCOZRM5j8PyP06kNcynTj0,1691
 loqusdb/build_models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 loqusdb/build_models/case.py,sha256=P3sfQkI_fH8u5iqecYWhV866lcHz4upWkepaea5MMIw,4255
 loqusdb/build_models/profile_variant.py,sha256=TbSxfVjESstS_FgbkOW4NQwMQVeTyhn9oc9yPZmDhzI,1021
-loqusdb/build_models/variant.py,sha256=JE3o_htRQjpwwUPxmP5HJ_0Ax8BwKp610uBIo3HTaVA,6671
+loqusdb/build_models/variant.py,sha256=LviEaovB_s_-jaLM64x0NzqzilFr__NPgv4Vf49Rhbk,6939
 loqusdb/commands/__init__.py,sha256=BXAN3UADgqPrkGczzjlLO9GyyQ96dnLnP7n92JlYHgo,603
 loqusdb/commands/annotate.py,sha256=748kImopE5WbaO1nuv3WUgIqezWFSsi7SBeWhOz26-s,1384
 loqusdb/commands/cli.py,sha256=wJD5S1BoCxtRTAobd1QtmQpzlngJg-mt1nsyD92fDD4,3176
@@ -46,9 +46,9 @@ loqusdb/utils/profiling.py,sha256=3OizF7CpYvSl9kyl2g4KGJxbIRUqWfmfLxn3843XYDk,91
 loqusdb/utils/update.py,sha256=1edJG-u24FgOSxyXAQEiyTG4IyK-Uo3lSIl5qyzcXsI,4433
 loqusdb/utils/variant.py,sha256=Lq5x9egVB-3rExBiRceF67TaL4Hp2gGoWMSRBEcnm4Q,2088
 loqusdb/utils/vcf.py,sha256=ybmrTBEPYa0FbUXo8ttlwATk13RnKjX9eIDbRDwCiVE,5175
-loqusdb-2.7.3.dist-info/LICENSE,sha256=urpFcJXw3elN9kV2fFutc-lXegjuu2lqP_GSy8_CAbs,1054
-loqusdb-2.7.3.dist-info/METADATA,sha256=zgf3S9hSpX0PXSt6M2aZoiNN9fAuemQ1jB4WcWnrMv0,6007
-loqusdb-2.7.3.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-loqusdb-2.7.3.dist-info/entry_points.txt,sha256=39QklW01vy9ilBLcRPgCP18kN6oKXXLoOK50gZE7Jbs,59
-loqusdb-2.7.3.dist-info/top_level.txt,sha256=lRdRO6hqPhJEjFhfNsbCgVWMztvkYsjiOGK9DAL0UAI,8
-loqusdb-2.7.3.dist-info/RECORD,,
+loqusdb-2.7.4.dist-info/LICENSE,sha256=urpFcJXw3elN9kV2fFutc-lXegjuu2lqP_GSy8_CAbs,1054
+loqusdb-2.7.4.dist-info/METADATA,sha256=XxP5xaw8eJa0wWxJn2DCLk9aSd3P2f69-K9s4mw4lSU,6007
+loqusdb-2.7.4.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+loqusdb-2.7.4.dist-info/entry_points.txt,sha256=39QklW01vy9ilBLcRPgCP18kN6oKXXLoOK50gZE7Jbs,59
+loqusdb-2.7.4.dist-info/top_level.txt,sha256=lRdRO6hqPhJEjFhfNsbCgVWMztvkYsjiOGK9DAL0UAI,8
+loqusdb-2.7.4.dist-info/RECORD,,

{loqusdb-2.7.3.dist-info → loqusdb-2.7.4.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.2)
+Generator: bdist_wheel (0.43.0)
 Root-Is-Purelib: true
 Tag: py3-none-any