loqusdb 2.7.2__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/commands/export.py

@@ -39,7 +39,6 @@ def export(ctx, outfile, variant_type, freq):
     version = ctx.obj["version"]
 
     LOG.info("Export the variants from {0}".format(adapter))
-    nr_cases = 0
 
     is_sv = variant_type == "sv"
     existing_chromosomes = set(adapter.get_chromosomes(sv=is_sv))
@@ -52,8 +51,8 @@ def export(ctx, outfile, variant_type, freq):
     for chrom in existing_chromosomes:
         ordered_chromosomes.append(chrom)
 
-    nr_cases = adapter.cases().count()
-    LOG.info("Found {0} cases in database".format(nr_cases))
+    nr_cases = adapter.case_count()
+    LOG.info(f"Found {nr_cases} cases in database")
 
     head = HeaderParser()
     head.add_fileformat("VCFv4.3")
@@ -85,7 +84,7 @@ def export(ctx, outfile, variant_type, freq):
         else:
             LOG.info("Collecting all SV variants")
             variants = adapter.get_sv_variants(chromosome=chrom)
-        LOG.info("{} variants found".format(variants.count()))
+        LOG.info(f"{adapter.nr_variants(chromosome=chrom)} variants found")
         for variant in variants:
             variant_line = format_variant(
                 variant, variant_type=variant_type, nr_cases=nr_cases, add_freq=freq

loqusdb/commands/identity.py

@@ -17,13 +17,12 @@ def identity(ctx, variant_id):
         ctx.abort()
 
     adapter = ctx.obj["adapter"]
-    version = ctx.obj["version"]
 
     LOG.info("Search variants {0}".format(adapter))
 
-    result = adapter.get_clusters(variant_id)
-    if result.count() == 0:
-        LOG.info("No hits for variant %s", variant_id)
+    variant_count: int = adapter.db.identity.count_documents({"variant_id": variant_id})
+    if variant_count == 0:
+        LOG.info(f"No hits for variant {variant_id}")
         return
 
     for res in result:

loqusdb/commands/view.py

@@ -2,6 +2,7 @@
 import json
 import logging
 from pprint import pprint as pp
+from pymongo.cursor import Cursor
 
 import click
 
@@ -42,10 +43,12 @@ def cases(ctx, case_id, to_json, count, case_type):
         case_obj["_id"] = str(case_obj["_id"])
         cases.append(case_obj)
     else:
-        cases = adapter.cases()
-        if cases.count() == 0:
+        case_count: int = adapter.case_count()
+        if case_count == 0:
             LOG.info("No cases found in database")
             ctx.abort()
+        cases: Cursor = adapter.cases()
+
 
     if to_json:
         click.echo(json.dumps(cases))

loqusdb/plugins/mongo/case.py

@@ -99,13 +99,6 @@ class CaseMixin:
         LOG.info("Removing case {0} from database".format(mongo_case.get("case_id")))
         self.db.case.delete_one({"_id": mongo_case["_id"]})
 
-    def case_count(self):
-        """Returns the total number of cases in the database
-
-        returns:
-            nr_of_cases (int): Total number of cases in database
-        """
-        nr_of_cases = 0
-        res = self.cases
-
-        return res.count()
+    def case_count(self) -> int:
+        """Returns the total number of cases in the database."""
+        return self.db.case.count_documents({})

{loqusdb-2.7.2.dist-info → loqusdb-2.7.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: loqusdb
-Version: 2.7.2
+Version: 2.7.4
 Summary: Store observations of vcf variants in a mongodb
 Home-page: https://github.com/moonso/loqusdb
 Author: Måns Magnusson
@@ -22,16 +22,16 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: pytest ==5.4.3
 Requires-Dist: cyvcf2 ==0.30.12
-Requires-Dist: mongomock ==3.18.0
+Requires-Dist: mongomock
 Requires-Dist: click ==7.1.2
-Requires-Dist: pymongo ==3.7.1
+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
-Requires-Dist: mongo-adapter >=0.3.3
+Requires-Dist: mongo-adapter
 Requires-Dist: ped-parser
 
 

{loqusdb-2.7.2.dist-info → loqusdb-2.7.4.dist-info}/RECORD

@@ -4,19 +4,19 @@ 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
 loqusdb/commands/delete.py,sha256=R6ysHKSMw1mmL4ZbktoUIKzdzDLQ3314YPYhIy1myic,1979
-loqusdb/commands/export.py,sha256=0V3S3QU9LKlR13w3KCGfqFliTYiDRCgNwusA27AEvmE,3254
-loqusdb/commands/identity.py,sha256=hzbnvniKgSNEwSeYHsxdNvVlqu_vXeOSLlNFnDXTQjA,779
+loqusdb/commands/export.py,sha256=-9SHgvr0G8FlyW0FGSfe1dmNDnjx4HKAaa-xYzSkvNc,3238
+loqusdb/commands/identity.py,sha256=KLA9c8e6cJFDxtqIa1G6zdHTHK1sz2b3v1Utdtik_4k,787
 loqusdb/commands/load.py,sha256=cVDdY7meBfcv8nMEGsjAX6aE-SKDOceGqM2vAvXPhko,4407
 loqusdb/commands/load_profile.py,sha256=cflCbF9f77_HCH8xPnN8zSSocvIffRMnC2LPE0j7Xq8,3336
 loqusdb/commands/migrate.py,sha256=2C8YL-zVqnpnqg3JIyUr0rbVnb8-AGPVWNhicHnPKLo,667
 loqusdb/commands/restore.py,sha256=eqPX0yao0IAYS5SbjCdlsfSJRBbRByBLISUU2hTzqqs,1492
 loqusdb/commands/update.py,sha256=zz3wueaJVqJ1FKact-rpY2az__5oa1LnZKf7mgqNGPk,3211
-loqusdb/commands/view.py,sha256=zQag5kgvUFa8nW9OVte_qjit0n8wGLc3C3hwLOMGY6o,5111
+loqusdb/commands/view.py,sha256=kQ_HuFhIX5wTHoEFC6atH-5unQFkRtopzD2_GqHNPKY,5198
 loqusdb/commands/wipe.py,sha256=WTOjyNooCUhtmZ6pdcPFa0PZrFc9E_pkLbnat_zP96M,553
 loqusdb/constants/__init__.py,sha256=r6y2TN8BqbKuh2Uyxq0trh-3A9xiWeStqWlvEPp-rSA,1645
 loqusdb/exceptions/__init__.py,sha256=Fq0UQg9TepWh19D7WT3dARyAHvorwJF6phhnZi2AkxE,88
@@ -31,7 +31,7 @@ loqusdb/models/variant.py,sha256=9QpM0ojJ24tKY9RrcgC411Wjnl3uRUawVYo6RWz1gXY,106
 loqusdb/plugins/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 loqusdb/plugins/mongo/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 loqusdb/plugins/mongo/adapter.py,sha256=rRUQ2y_bZwjINbdTtfzJ_1JwE0Ns0usyAJ3o0O1Y10I,2593
-loqusdb/plugins/mongo/case.py,sha256=_LslGBB0F50IpjeEoV234JszC5TihAqFK3LBPMVD71k,3119
+loqusdb/plugins/mongo/case.py,sha256=zKnaaam8Ey1AEH-1GofXp6iNqgmSvWWxZZWsx7dAO0Y,3006
 loqusdb/plugins/mongo/profile_variant.py,sha256=madOBa3HacIN_T1V8mp7NEC4QOpqQBqSY6pKTObkMLA,600
 loqusdb/plugins/mongo/structural_variant.py,sha256=RPc3GF37-O3GqRS9Z5PRxsBXACljfRT4KFsrEl0jCu0,12955
 loqusdb/plugins/mongo/variant.py,sha256=NS3N8bhRap1b2ZSGjOw2LO6l7q_CzD00GZs499l38Tg,8715
@@ -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-2.7.2.dist-info/LICENSE,sha256=urpFcJXw3elN9kV2fFutc-lXegjuu2lqP_GSy8_CAbs,1054
-loqusdb-2.7.2.dist-info/METADATA,sha256=NvWYugvrSe_lUtPGvWwXxUnqc-OiY0eJSRJ31gtatYk,6032
-loqusdb-2.7.2.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-loqusdb-2.7.2.dist-info/entry_points.txt,sha256=39QklW01vy9ilBLcRPgCP18kN6oKXXLoOK50gZE7Jbs,59
-loqusdb-2.7.2.dist-info/top_level.txt,sha256=lRdRO6hqPhJEjFhfNsbCgVWMztvkYsjiOGK9DAL0UAI,8
-loqusdb-2.7.2.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-2.7.2.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