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update beacon import function to be able to extract data from galaxy …
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…and change script name
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@khaled196
khaled196 committed Nov 17, 2023
1 parent b46449d commit 7f2b845
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Showing 4 changed files with 612 additions and 124 deletions.
225 changes: 154 additions & 71 deletions beacon_search.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,91 +9,174 @@ def beacon_query():

# Sub-parser for command "Beacon Sequence Queries"
parser_sequence = subparsers.add_parser('sequence_queries')
parser_sequence.add_argument('-c', '--collection', type=str, default='', help="The targeted beacon collection")
parser_sequence.add_argument('-d', '--dataset', type=str, default='', help="The targeted beacon dataset from the desired collection")
parser_sequence.add_argument('-I', '--db_ip', type=str, default='127.0.0.1', help='Input MongoDB IP address')
parser_sequence.add_argument("-P", "--db-port", type=int, default="27017", dest="database_port", help="port of the beacon database")
parser_sequence.add_argument("-r", "--referenceName", type=str, default='', help='Reference name')
parser_sequence.add_argument("-s", "--start", type=int, default='', help='Start')
parser_sequence.add_argument("-a", "--alternateBases", type=str, default='', help='Alternate Bases')
parser_sequence.add_argument("-rb", "--referenceBases", type=str, default='', help='Reference Bases')
parser_sequence.add_argument("-id", "--datasetIds", type=str, default='', help='dataset Id')
parser_sequence.add_argument('-c', '--collection', type=str, default='', dest='collection', help="The targeted beacon collection")
parser_sequence.add_argument('-d', '--dataset', type=str, default='', dest='dataset', help="The targeted beacon dataset from the desired collection")
parser_sequence.add_argument('-I', '--db-ip', type=str, default='127.0.0.1', dest='db_ip', help='Input MongoDB IP address')
parser_sequence.add_argument("-P", "--db-port", type=int, default="27017", dest='db_port', dest="database_port", help="port of the beacon database")
parser_sequence.add_argument("-rn", "--referenceName", type=str, default='', dest='referenceName', help='Reference name')
parser_sequence.add_argument("-s", "--start", type=int, default='', dest='start', help='Start')
parser_sequence.add_argument("-ab", "--alternateBases", type=str, default='', dest='alternateBases', help='Alternate Bases')
parser_sequence.add_argument("-rb", "--referenceBases", type=str, default='', dest='referenceBases', help='Reference Bases')
parser_sequence.add_argument("-id", "--datasetIds", type=str, default='', dest='datasetIds', help='dataset Id') # optional

# Sub-parser for command "Beacon Range Queries"
parser_range = subparsers.add_parser('range_queries')
parser_range.add_argument('-c', '--collection', type=str, default='', help="The targeted beacon collection")
parser_range.add_argument('-d', '--dataset', type=str, default='', help="The targeted beacon dataset from the desired collection")
parser_range.add_argument('-I', '--db_ip', type=str, default='127.0.0.1', help='Input MongoDB IP address')
parser_range.add_argument("-P", "--db-port", type=int, default="27017", dest="database_port", help="port of the beacon database")
parser_range.add_argument("-r", "--referenceName", type=str, default='', help='Reference name')
parser_range.add_argument("-s", "--start", type=int, default='', help='Start')
parser_range.add_argument("-e", "--end", type=int, default='', help='END')
parser_range.add_argument("-a", "--alternateBases", type=str, default='', help='Alternate Bases')
parser_range.add_argument("-rb", "--variantType", type=str, default='', help='Variant Type')
parser_range.add_argument("-id", "--aminoacidChange", type=str, default='', help='Aminoacid Change')
parser_range.add_argument("-max", "--variantMinLength", type=int, default='', help='Variant Minimum Length')
parser_range.add_argument("-min", "--variantMaxLength", type=int, default='', help='variant Maximum Length')
parser_range.add_argument('-c', '--collection', type=str, default='', dest='collection', help="The targeted beacon collection")
parser_range.add_argument('-d', '--dataset', type=str, default='', dest='dataset', help="The targeted beacon dataset from the desired collection")
parser_range.add_argument('-I', '--db-ip', type=str, default='127.0.0.1', dest='db_ip', help='Input MongoDB IP address')
parser_range.add_argument("-P", "--db-port", type=int, default="27017", dest="db_port", help="port of the beacon database")
parser_range.add_argument("-rn", "--referenceName", type=str, default='', dest='referenceName', help='Reference name')
parser_range.add_argument("-s", "--start", type=int, default='', dest='start', help='Start')
parser_range.add_argument("-e", "--end", type=int, default='', dest='end', help='END')
parser_range.add_argument("-ab", "--alternateBases", type=str, default='', dest='alternateBases', help='Alternate Bases') #
parser_range.add_argument("-v", "--variantType", type=str, default='', dest='variantType', help='Variant Type')
parser_range.add_argument("-ac", "--aminoacidChange", type=str, default='', dest='aminoacidChange', help='Aminoacid Change')
parser_range.add_argument("vmax", "--variantMinLength", type=int, default='', dest='variantMinLength', help='Variant Minimum Length')
parser_range.add_argument("vmin", "--variantMaxLength", type=int, default='', dest='variantMaxLength', help='variant Maximum Length')

# Sub-parser for command "Beacon GeneId Queries"
parser_gene = subparsers.add_parser('gene_id_queries')
parser_gene.add_argument('-c', '--collection', type=str, default='', help="The targeted beacon collection")
parser_gene.add_argument('-d', '--dataset', type=str, default='', help="The targeted beacon dataset from the desired collection")
parser_gene.add_argument('-I', '--db_ip', type=str, default='127.0.0.1', help='Input MongoDB IP address')
parser_gene.add_argument("-P", "--db-port", type=int, default="27017", dest="database_port", help="port of the beacon database")
parser_gene.add_argument("-g", "--geneId", type=str, default='', help='Gene ID')
parser_gene.add_argument("-a", "--alternateBases", type=str, default='', help='Alternate Bases')
parser_gene.add_argument("-rb", "--variantType", type=str, default='', help='Variant Type')
parser_gene.add_argument("-id", "--aminoacidChange", type=str, default='', help='Aminoacid Change')
parser_gene.add_argument("-max", "--variantMinLength", type=int, default='', help='Variant Minimum Length')
parser_gene.add_argument("-min", "--variantMaxLength", type=int, default='', help='variant Maximum Length')
parser_gene.add_argument('-c', '--collection', type=str, default='', dest='collection', help="The targeted beacon collection")
parser_gene.add_argument('-d', '--dataset', type=str, default='', dest='dataset', help="The targeted beacon dataset from the desired collection")
parser_gene.add_argument('-I', '--db-ip', type=str, default='127.0.0.1', dest='db_ip', help='Input MongoDB IP address')
parser_gene.add_argument("-P", "--db-port", type=int, default="27017", dest="db_port", help="port of the beacon database")
parser_gene.add_argument("-g", "--geneId", type=str, default='', dest='geneId', help='Gene ID')
parser_gene.add_argument("-ab", "--alternateBases", type=str, default='', dest='alternateBases', help='Alternate Bases')
parser_gene.add_argument("-v", "--variantType", type=str, default='', dest='variantType', help='Variant Type')
parser_gene.add_argument("-ac", "--aminoacidChange", type=str, default='', dest='aminoacidChange', help='Aminoacid Change')
parser_gene.add_argument("vmax", "--variantMinLength", type=int, default='', dest='variantMinLength', help='Variant Minimum Length')
parser_gene.add_argument("vmin", "--variantMaxLength", type=int, default='', dest='variantMaxLength', help='variant Maximum Length')

# Sub-parser for command "Beacon Bracket Queries"
parser_bracket = subparsers.add_parser('bracket_queries')
parser_bracket.add_argument('-c', '--collection', type=str, default='', help="The targeted beacon collection")
parser_bracket.add_argument('-d', '--dataset', type=str, default='', help="The targeted beacon dataset from the desired collection")
parser_bracket.add_argument('-I', '--db_ip', type=str, default='127.0.0.1', help='Input MongoDB IP address')
parser_bracket.add_argument("-P", "--db-port", type=int, default="27017", dest="database_port", help="port of the beacon database")
parser_bracket.add_argument("-r", "--referenceName", type=str, default='', help='Reference name')
parser_bracket.add_argument("-s-min", "--start-minimum", type=int, default='', help='Start Minimum')
parser_bracket.add_argument("-s-max", "--start-maximum", type=int, default='', help='Start maximum')
parser_bracket.add_argument("-e-min", "--end-minimum", type=int, default='', help='END Minimum')
parser_bracket.add_argument("-e-max", "--end-maximum", type=int, default='', help='END maximum')
parser_bracket.add_argument("-rb", "--variantType", type=str, default='', help='Variant Type')
parser_bracket.add_argument('-c', '--collection', type=str, default='', dest='collection', help="The targeted beacon collection")
parser_bracket.add_argument('-d', '--dataset', type=str, default='', dest='dataset', help="The targeted beacon dataset from the desired collection")
parser_bracket.add_argument('-I', '--db-ip', type=str, default='127.0.0.1', dest='db_ip', help='Input MongoDB IP address')
parser_bracket.add_argument("-P", "--db-port", type=int, default="27017", dest="db_port", help="port of the beacon database")
parser_bracket.add_argument("-rn", "--referenceName", type=str, default='', dest='referenceName', help='Reference name')
parser_bracket.add_argument("-smin", "--start-minimum", type=int, default='', dest='start_minimum', help='Start Minimum')
parser_bracket.add_argument("-smax", "--start-maximum", type=int, default='', dest='start_maximum', help='Start maximum')
parser_bracket.add_argument("-emin", "--end-minimum", type=int, default='', dest='end_minimum', help='END Minimum')
parser_bracket.add_argument("-emax", "--end-maximum", type=int, default='', dest='end_maximum', help='END maximum')
parser_bracket.add_argument("-v", "--variantType", type=str, default='', dest='variantType', help='Variant Type')

args = parser.parse_args()

client = MongoClient(args.db_ip, args.database_port)
db = client.cnv
sample = db.sample1

# Example query based on command
if args.command == 'sequence_queries':
for v in sample.find({'start': args.start, 'end': args.end}):
# query sequence_queries
if args.command == 'sequence':
client = MongoClient(args.db_ip, args.db_port)
db = client[args.collection]
sample = db[args.dataset]
query = {
'referenceName': args.referenceName,
'start': args.start,
'alternateBases': args.alternateBases,
'referenceBases': args.referenceBases,
'datasetIds': args.datasetIds
}
# Create a new dictionary with non-empty and non-default values
filtered_query = {key: value for key, value in query.items() if value}
# if not args.datasetIds:
# query= {'referenceName': args.referenceName, 'start': args.start, 'alternateBases':args.alternateBases , 'referenceBases':args.referenceBases}
# else:
# query= {'referenceName': args.referenceName, 'start': args.start, 'alternateBases':args.alternateBases , 'referenceBases':args.referenceBases, 'datasetIds': args.datasetIds}
for v in sample.find(filtered_query):
pprint.pprint(v)
elif args.command == 'range_queries':
# Add logic for range_queries
pass
elif args.command == 'gene_id_queries':
# Add logic for gene_id_queries
pass
elif args.command == 'bracket_queries':
# Add logic for bracket_queries
pass

if __name__ == "__main__":
beacon_query()

# client = MongoClient("127.0.0.1", 27017)
# db = client.cnv
# sample = db.sample1

#sample.find({'start': 11744914})
# query range_queries

elif args.command == 'range':
if args.command == 'range':
client = MongoClient(args.db_ip, args.db_port)
db = client[args.collection]
sample = db[args.dataset]
query = {
'referenceName': args.referenceName,
'start': args.start,
'end': args.end,
'variantType': args.variantType,
'alternateBases': args.alternateBases,
'aminoacidChange':args.aminoacidChange,
'variantMinLength':args.variantMinLength,
'variantMaxLength':args.variantMaxLength
}
# Create a new dictionary with non-empty and non-default values
filtered_query = {key: value for key, value in query.items() if value}
# if not args.alternateBases, args.variantType, args.aminoacidChange, args.variantMinLength, args.variantMaxLength:
# query= {'referenceName': args.referenceName, 'start': args.start, 'end':args.end}
# elif not args.variantType, args.aminoacidChange, args.variantMinLength, args.variantMaxLength:
# query= {'referenceName': args.referenceName, 'start': args.start, 'end':args.end, 'alternateBases':args.alternateBases}
# elif not args.alternateBases, args.aminoacidChange, args.variantMinLength, args.variantMaxLength:
# query= {'referenceName': args.referenceName, 'start': args.start, 'end':args.end, 'variantType':args.variantType}
# elif not args.alternateBases, args.aminoacidChange, args.variantMaxLength:
# query= {'referenceName': args.referenceName, 'start': args.start, 'end':args.end, 'variantType':args.variantType, 'variantMinLength':args.variantMinLength}
# elif not args.alternateBases, args.aminoacidChange:
# query= {'referenceName': args.referenceName, 'start': args.start, 'end':args.end, 'variantType':args.variantType, 'variantMinLength':args.variantMinLength, 'variantMaxLength':args.variantMaxLength}
# elif not args.variantType, args.alternateBases, args.variantMinLength, args.variantMaxLength:
# query= {'referenceName': args.referenceName, 'start': args.start, 'end':args.end, 'aminoacidChange':args.aminoacidChange}
for v in sample.find(filtered_query):
pprint.pprint(v)

# for v in sample.find({'start': 11744914, 'end': 11748800}):
# pprint.pprint(v)
# query gene_id_queries
elif args.command == 'gene_id':
if args.command == 'gene_id':
client = MongoClient(args.db_ip, args.db_port)
db = client[args.collection]
sample = db[args.dataset]
query = {
'geneId': args.geneId,
'variantType': args.variantType,
'alternateBases': args.alternateBases,
'aminoacidChange':args.aminoacidChange,
'variantMinLength':args.variantMinLength,
'variantMaxLength':args.variantMaxLength
}
# Create a new dictionary with non-empty and non-default values
filtered_query = {key: value for key, value in query.items() if value}
# if not args.alternateBases, args.variantType, args.aminoacidChange, args.variantMinLength, args.variantMaxLength:
# query= {'geneId': args.geneId}
# elif not args.variantType, args.aminoacidChange, args.variantMinLength, args.variantMaxLength:
# query= {'geneId': args.geneId, 'alternateBases':args.alternateBases}
# elif not args.alternateBases, args.aminoacidChange, args.variantMinLength, args.variantMaxLength:
# query= {'geneId': args.geneId, 'variantType':args.variantType}
# elif not args.alternateBases, args.variantMinLength, args.variantMaxLength:
# query= {'geneId': args.geneId, 'variantType':args.variantType 'aminoacidChange':args.aminoacidChange}
# elif not args.alternateBases, args.aminoacidChange, args.variantMaxLength:
# query= {'geneId': args.geneId, 'variantType':args.variantType, 'variantMinLength':args.variantMinLength}
# elif not args.alternateBases, args.aminoacidChange, args.variantMinLength:
# query= {'geneId': args.geneId, 'variantType':args.variantType, 'variantMaxLength':args.variantMaxLength}
# elif not args.alternateBases, args.variantMaxLength:
# query= {'geneId': args.geneId, 'variantType':args.variantType 'aminoacidChange':args.aminoacidChange, 'variantMinLength':args.variantMinLength}
# elif not args.alternateBases, args.aminoacidChange:
# query= {'geneId': args.geneId, 'variantType':args.variantType, 'variantMinLength':args.variantMinLength, 'variantMaxLength':args.variantMaxLength}
# elif not args.alternateBases:
# query= {'geneId': args.geneId, 'variantType':args.variantType, 'aminoacidChange':args.aminoacidChange, 'variantMinLength':args.variantMinLength, 'variantMaxLength':args.variantMaxLength}
# elif not args.variantType, args.alternateBases, args.variantMinLength, args.variantMaxLength:
# query= {'geneId': args.geneId, 'aminoacidChange':args.aminoacidChange}
for v in sample.find(filtered_query):
pprint.pprint(v)
# query bracket_queries
elif args.command == 'bracket':
if args.command == 'bracket':
client = MongoClient(args.db_ip, args.db_port)
db = client[args.collection]
sample = db[args.dataset]
query = {
'referenceName': args.geneId,
'start': args.start_minimum,
'start': args.start_maximum,
'end':args.end_minimum,
'end':args.end_maximum,
'variantType':args.variantType
}
# Create a new dictionary with non-empty and non-default values
filtered_query = {key: value for key, value in query.items() if value}
# if not args.variantType:
# query= {'referenceName': args.referenceName, 'start': args.start_minimum, 'start': args.start_maximum, 'end':args.end_minimum, 'end':args.end_maximum}
# else:
# query= {'referenceName': args.referenceName, 'start': args.start_minimum, 'start': args.start_maximum, 'end':args.end_minimum, 'end':args.end_maximum, 'variantType':args.variantType}
for v in sample.find(filtered_query):
pprint.pprint(v)

#pprint.pprint(sample.find_one())
#print(sample.list_collection_names())
#if __name__ == "__main__":
# beacon_query()
if __name__ == "__main__":
beacon_query()
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