Merge pull request #22 from EGA-archive/zygosity

Adding zygosity queries

beacon/connections/mongo/analyses.py

@@ -71,7 +71,19 @@ def get_variants_of_analysis(self, entry_id: Optional[str], qparams: RequestPara
         schema = DefaultSchemas.GENOMICVARIATIONS
         return schema, 0, -1, None, dataset
     position=str(position)
-    query_cl={ position: "y", "datasetId": dataset}
+    filters=qparams.query.filters
+    if filters != []:
+        for filter in filters:
+            if filter['id']=='GENO:GENO_0000458':
+                query_cl={"$or": [{ position: "10", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
+                qparams.query.filters.remove(filter)
+            elif filter['id']=='GENO:GENO_0000136':
+                query_cl={"$or": [{ position: "11", "datasetId": dataset}]}
+                qparams.query.filters.remove(filter)
+            else:
+                query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
+    else:
+        query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
     string_of_ids = client.beacon.caseLevelData \
         .find(query_cl, {"id": 1, "_id": 0}).limit(qparams.query.pagination.limit).skip(qparams.query.pagination.skip)
     HGVSIds=list(string_of_ids)

beacon/connections/mongo/biosamples.py

@@ -66,7 +66,19 @@ def get_variants_of_biosample(self, entry_id: Optional[str], qparams: RequestPar
         schema = DefaultSchemas.GENOMICVARIATIONS
         return schema, 0, -1, None, dataset
     position=str(position)
-    query_cl={ position: "y", "datasetId": dataset}
+    filters=qparams.query.filters
+    if filters != []:
+        for filter in filters:
+            if filter['id']=='GENO:GENO_0000458':
+                query_cl={"$or": [{ position: "10", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
+                qparams.query.filters.remove(filter)
+            elif filter['id']=='GENO:GENO_0000136':
+                query_cl={"$or": [{ position: "11", "datasetId": dataset}]}
+                qparams.query.filters.remove(filter)
+            else:
+                query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
+    else:
+        query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
     string_of_ids = client.beacon.caseLevelData \
         .find(query_cl, {"id": 1, "_id": 0}).limit(qparams.query.pagination.limit).skip(qparams.query.pagination.skip)
     HGVSIds=list(string_of_ids)

beacon/connections/mongo/g_variants.py

@@ -87,9 +87,27 @@ def get_biosamples_of_variant(self, entry_id: Optional[str], qparams: RequestPar
     list_of_targets=targets[0]["biosampleIds"]
     list_of_positions_strings= string_of_ids[0]
     biosampleIds=[]
-    for key, value in list_of_positions_strings.items():
-        if key != 'datasetId' and key != 'id' and key != '_id':
-            biosampleIds.append(list_of_targets[int(key)])
+    filters=qparams.query.filters
+    if filters != []:
+        for filter in filters:
+            if filter['id']=='GENO:GENO_0000458':
+                for key, value in list_of_positions_strings.items():
+                    if key != 'datasetId' and key != 'id' and key != '_id' and value != '11':
+                        biosampleIds.append(list_of_targets[int(key)])
+                qparams.query.filters.remove(filter)
+            elif filter['id']=='GENO:GENO_0000136':
+                for key, value in list_of_positions_strings.items():
+                    if key != 'datasetId' and key != 'id' and key != '_id' and value != '10' and value != '01':
+                        biosampleIds.append(list_of_targets[int(key)])
+                qparams.query.filters.remove(filter)
+            else:
+                for key, value in list_of_positions_strings.items():
+                    if key != 'datasetId' and key != 'id' and key != '_id':
+                        biosampleIds.append(list_of_targets[int(key)])
+    else:
+        for key, value in list_of_positions_strings.items():
+            if key != 'datasetId' and key != 'id' and key != '_id':
+                biosampleIds.append(list_of_targets[int(key)])
     finalids=biosampleIds
     try:
         finalids=[]
@@ -138,9 +156,27 @@ def get_runs_of_variant(self, entry_id: Optional[str], qparams: RequestParams, d
     list_of_targets=targets[0]["biosampleIds"]
     list_of_positions_strings= string_of_ids[0]
     biosampleIds=[]
-    for key, value in list_of_positions_strings.items():
-        if key != 'datasetId' and key != 'id' and key != '_id':
-            biosampleIds.append(list_of_targets[int(key)])
+    filters=qparams.query.filters
+    if filters != []:
+        for filter in filters:
+            if filter['id']=='GENO:GENO_0000458':
+                for key, value in list_of_positions_strings.items():
+                    if key != 'datasetId' and key != 'id' and key != '_id' and value != '11':
+                        biosampleIds.append(list_of_targets[int(key)])
+                qparams.query.filters.remove(filter)
+            elif filter['id']=='GENO:GENO_0000136':
+                for key, value in list_of_positions_strings.items():
+                    if key != 'datasetId' and key != 'id' and key != '_id' and value != '10' and value != '01':
+                        biosampleIds.append(list_of_targets[int(key)])
+                qparams.query.filters.remove(filter)
+            else:
+                for key, value in list_of_positions_strings.items():
+                    if key != 'datasetId' and key != 'id' and key != '_id':
+                        biosampleIds.append(list_of_targets[int(key)])
+    else:
+        for key, value in list_of_positions_strings.items():
+            if key != 'datasetId' and key != 'id' and key != '_id':
+                biosampleIds.append(list_of_targets[int(key)])
     try:
         finalids=[]
         for bioid in biosampleIds:
@@ -188,9 +224,27 @@ def get_analyses_of_variant(self, entry_id: Optional[str], qparams: RequestParam
     list_of_targets=targets[0]["biosampleIds"]
     list_of_positions_strings= string_of_ids[0]
     biosampleIds=[]
-    for key, value in list_of_positions_strings.items():
-        if key != 'datasetId' and key != 'id' and key != '_id':
-            biosampleIds.append(list_of_targets[int(key)])
+    filters=qparams.query.filters
+    if filters != []:
+        for filter in filters:
+            if filter['id']=='GENO:GENO_0000458':
+                for key, value in list_of_positions_strings.items():
+                    if key != 'datasetId' and key != 'id' and key != '_id' and value != '11':
+                        biosampleIds.append(list_of_targets[int(key)])
+                qparams.query.filters.remove(filter)
+            elif filter['id']=='GENO:GENO_0000136':
+                for key, value in list_of_positions_strings.items():
+                    if key != 'datasetId' and key != 'id' and key != '_id' and value != '10' and value != '01':
+                        biosampleIds.append(list_of_targets[int(key)])
+                qparams.query.filters.remove(filter)
+            else:
+                for key, value in list_of_positions_strings.items():
+                    if key != 'datasetId' and key != 'id' and key != '_id':
+                        biosampleIds.append(list_of_targets[int(key)])
+    else:
+        for key, value in list_of_positions_strings.items():
+            if key != 'datasetId' and key != 'id' and key != '_id':
+                biosampleIds.append(list_of_targets[int(key)])
     try:
         finalids=[]
         for bioid in biosampleIds:
@@ -238,9 +292,27 @@ def get_individuals_of_variant(self, entry_id: Optional[str], qparams: RequestPa
     list_of_targets=targets[0]["biosampleIds"]
     list_of_positions_strings= string_of_ids[0]
     biosampleIds=[]
-    for key, value in list_of_positions_strings.items():
-        if key != 'datasetId' and key != 'id' and key != '_id':
-            biosampleIds.append(list_of_targets[int(key)])
+    filters=qparams.query.filters
+    if filters != []:
+        for filter in filters:
+            if filter['id']=='GENO:GENO_0000458':
+                for key, value in list_of_positions_strings.items():
+                    if key != 'datasetId' and key != 'id' and key != '_id' and value != '11':
+                        biosampleIds.append(list_of_targets[int(key)])
+                qparams.query.filters.remove(filter)
+            elif filter['id']=='GENO:GENO_0000136':
+                for key, value in list_of_positions_strings.items():
+                    if key != 'datasetId' and key != 'id' and key != '_id' and value != '10' and value != '01':
+                        biosampleIds.append(list_of_targets[int(key)])
+                qparams.query.filters.remove(filter)
+            else:
+                for key, value in list_of_positions_strings.items():
+                    if key != 'datasetId' and key != 'id' and key != '_id':
+                        biosampleIds.append(list_of_targets[int(key)])
+    else:
+        for key, value in list_of_positions_strings.items():
+            if key != 'datasetId' and key != 'id' and key != '_id':
+                biosampleIds.append(list_of_targets[int(key)])
     try:
         finalquery={}
         finalquery["$or"]=[]

beacon/connections/mongo/individuals.py

@@ -66,7 +66,19 @@ def get_variants_of_individual(self, entry_id: Optional[str], qparams: RequestPa
         schema = DefaultSchemas.GENOMICVARIATIONS
         return schema, 0, -1, None, dataset
     position=str(position)
-    query_cl={ position: "y", "datasetId": dataset}
+    filters=qparams.query.filters
+    if filters != []:
+        for filter in filters:
+            if filter['id']=='GENO:GENO_0000458':
+                query_cl={"$or": [{ position: "10", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
+                qparams.query.filters.remove(filter)
+            elif filter['id']=='GENO:GENO_0000136':
+                query_cl={"$or": [{ position: "11", "datasetId": dataset}]}
+                qparams.query.filters.remove(filter)
+            else:
+                query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
+    else:
+        query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
     string_of_ids = client.beacon.caseLevelData \
         .find(query_cl, {"id": 1, "_id": 0}).limit(qparams.query.pagination.limit).skip(qparams.query.pagination.skip)
     HGVSIds=list(string_of_ids)

beacon/connections/mongo/runs.py

@@ -67,7 +67,19 @@ def get_variants_of_run(self, entry_id: Optional[str], qparams: RequestParams, d
         schema = DefaultSchemas.GENOMICVARIATIONS
         return schema, 0, -1, None, dataset
     position=str(position)
-    query_cl={ position: "y", "datasetId": dataset}
+    filters=qparams.query.filters
+    if filters != []:
+        for filter in filters:
+            if filter['id']=='GENO:GENO_0000458':
+                query_cl={"$or": [{ position: "10", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
+                qparams.query.filters.remove(filter)
+            elif filter['id']=='GENO:GENO_0000136':
+                query_cl={"$or": [{ position: "11", "datasetId": dataset}]}
+                qparams.query.filters.remove(filter)
+            else:
+                query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
+    else:
+        query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
     string_of_ids = client.beacon.caseLevelData \
         .find(query_cl, {"id": 1, "_id": 0}).limit(qparams.query.pagination.limit).skip(qparams.query.pagination.skip)
     HGVSIds=list(string_of_ids)

docker-compose.yml

@@ -79,6 +79,9 @@ services:
     volumes:
       - ./beacon/connections/mongo/mongo-init/:/docker-entrypoint-initdb.d/:ro
       - ./beacon/connections/mongo/data/:/data
+      - ./beacon/connections/mongo/data/db:/data/db
+      - ./beacon/connections/mongo/data/configdb:/data/configdb
+      - ./beacon/connections/mongo/data/caseLevelData:/data/caseLevelData
     networks:
       - pub
     #command: --verbose

ri-tools/conf/conf.py

@@ -4,11 +4,12 @@
 
 #### VCF Conversion config parameters ####
 allele_frequency=1 # introduce float number, leave 1 if you want to convert all the variants
-reference_genome='GRCh37' # Choose one between NCBI36, GRCh37, GRCh38
+reference_genome='GRCh38' # Choose one between NCBI36, GRCh37, GRCh38
 datasetId='CINECA_synthetic_cohort_EUROPE_UK1'
 case_level_data=True
 num_rows=7000000
 population='Finnish'
+zygosity=True
 
 ### MongoDB parameters ###
 database_host = 'mongo'

ri-tools/output_docs/CINECA_synthetic_cohort_EUROPE_UK1/cohorts.json

@@ -1 +1,116 @@
-[{"cohortType": "study-defined", "collectionEvents": [{"eventDiseases": {"availability": true, "availabilityCount": 1705, "distribution": {"diseases": {"acutebronchitis": 121, "agranulocytosis": 111, "asthma": 134, "bipolaraffectivedisorder": 134, "cardiomyopathy": 133, "dentalcaries": 139, "eatingdisorders": 134, "fibrosisandcirrhosisofliver": 132, "gastro-oesophagealrefluxdisease": 140, "haemorrhoids": 127, "influenzaduetocertainidentifiedinfluenzavirus": 135, "insulin-dependentdiabetesmellitus": 165, "irondeficiencyanaemia": 142, "multiplesclerosis": 125, "obesity": 136, "sarcoidosis": 136, "schizophrenia": 138, "thyroiditis": 141, "varicoseveinsoflowerextremities": 139}}}, "eventEthnicities": {"availability": true, "availabilityCount": 2287, "distribution": {"ethnicities": {"African": 119, "AnyotherAsianbackground": 120, "AnyotherBlackbackground": 104, "Anyothermixedbackground": 92, "Anyotherwhitebackground": 114, "AsianorAsianBritish": 125, "Bangladeshi": 96, "BlackorBlackBritish": 131, "British": 114, "Caribbean": 127, "Chinese": 100, "Indian": 110, "Irish": 111, "Mixed": 127, "Otherethnicgroup": 116, "Pakistani": 115, "White": 105, "WhiteandAsian": 114, "WhiteandBlackAfrican": 115, "WhiteandBlackCaribbean": 132}}}, "eventGenders": {"availability": true, "availabilityCount": 1597, "distribution": {"genders": {"female": 1271, "male": 1233}}}}], "id": "CINECA_synthetic_cohort_UK1", "inclusionCriteria": {"ageRange": {"end": {"iso8601duration": "P65Y"}, "start": {"iso8601duration": "P18Y"}}, "genders": [{"id": "NCIT:C16576", "label": "female"}, {"id": "NCIT:C20197", "label": "male"}], "locations": [{"id": "GAZ:00150372", "label": "UK"}]}, "name": "CINECA synthetic cohort UK1"}]
+[
+    {
+        "datasetId": "CINECA_synthetic_cohort_EUROPE_UK1",
+        "cohortType": "study-defined",
+        "collectionEvents": [
+            {
+                "eventDiseases": {
+                    "availability": true,
+                    "availabilityCount": 1705,
+                    "distribution": {
+                        "diseases": {
+                            "acutebronchitis": 121,
+                            "agranulocytosis": 111,
+                            "asthma": 134,
+                            "bipolaraffectivedisorder": 134,
+                            "cardiomyopathy": 133,
+                            "dentalcaries": 139,
+                            "eatingdisorders": 134,
+                            "fibrosisandcirrhosisofliver": 132,
+                            "gastro-oesophagealrefluxdisease": 140,
+                            "haemorrhoids": 127,
+                            "influenzaduetocertainidentifiedinfluenzavirus": 135,
+                            "insulin-dependentdiabetesmellitus": 165,
+                            "irondeficiencyanaemia": 142,
+                            "multiplesclerosis": 125,
+                            "obesity": 136,
+                            "sarcoidosis": 136,
+                            "schizophrenia": 138,
+                            "thyroiditis": 141,
+                            "varicoseveinsoflowerextremities": 139
+                        }
+                    }
+                },
+                "eventEthnicities": {
+                    "availability": true,
+                    "availabilityCount": 2287,
+                    "distribution": {
+                        "ethnicities": {
+                            "African": 119,
+                            "AnyotherAsianbackground": 120,
+                            "AnyotherBlackbackground": 104,
+                            "Anyothermixedbackground": 92,
+                            "Anyotherwhitebackground": 114,
+                            "AsianorAsianBritish": 125,
+                            "Bangladeshi": 96,
+                            "BlackorBlackBritish": 131,
+                            "British": 114,
+                            "Caribbean": 127,
+                            "Chinese": 100,
+                            "Indian": 110,
+                            "Irish": 111,
+                            "Mixed": 127,
+                            "Otherethnicgroup": 116,
+                            "Pakistani": 115,
+                            "White": 105,
+                            "WhiteandAsian": 114,
+                            "WhiteandBlackAfrican": 115,
+                            "WhiteandBlackCaribbean": 132
+                        }
+                    }
+                },
+                "eventGenders": {
+                    "availability": true,
+                    "availabilityCount": 1597,
+                    "distribution": {
+                        "genders": {
+                            "female": 1271,
+                            "male": 1233
+                        }
+                    }
+                },
+                "eventLocations": {
+                    "availability": true,
+                    "availabilityCount": 1597,
+                    "distribution": {
+                        "locations": {
+                            "England": 322,
+                            "NorthernIreland": 317,
+                            "RepublicofIreland": 311,
+                            "Scotland": 308,
+                            "Wales": 339
+                        }
+                    }
+                }
+            }
+        ],
+        "id": "CINECA_synthetic_cohort_UK1",
+        "inclusionCriteria": {
+            "ageRange": {
+                "end": {
+                    "iso8601duration": "P65Y"
+                },
+                "start": {
+                    "iso8601duration": "P18Y"
+                }
+            },
+            "genders": [
+                {
+                    "id": "NCIT:C16576",
+                    "label": "female"
+                },
+                {
+                    "id": "NCIT:C20197",
+                    "label": "male"
+                }
+            ],
+            "locations": [
+                {
+                    "id": "GAZ:00150372",
+                    "label": "UK"
+                }
+            ]
+        },
+        "name": "CINECA synthetic cohort UK1"
+    }
+]

ri-tools/output_docs/CINECA_synthetic_cohort_EUROPE_UK1/filtering_terms.json

@@ -0,0 +1,23 @@
+[
+    {
+        "type": "alphanumeric",
+        "id": "libraryStrategy",
+        "scopes": [
+            "run"
+        ]
+    },
+    {
+        "type": "alphanumeric",
+        "id": "molecularAttributes.geneIds",
+        "scopes": [
+            "genomicVariation"
+        ]
+    },
+    {
+        "type": "alphanumeric",
+        "id": "diseases.ageOfOnset.iso8601duration",
+        "scopes": [
+            "individual"
+        ]
+    }
+]