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create the fuction skiliton// not ready to be used
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,99 @@ | ||
| from pymongo import MongoClient | ||
| import argparse | ||
| import pprint | ||
|
|
||
| def beacon_query(): | ||
| parser = argparse.ArgumentParser(description="Query Beacon Database") | ||
| subparsers = parser.add_subparsers(dest='command') | ||
| subparsers.required = True | ||
|
|
||
| # 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') | ||
|
|
||
| # 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') | ||
|
|
||
| # 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') | ||
|
|
||
| # 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') | ||
|
|
||
| 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}): | ||
| 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 | ||
|
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||
| #sample.find({'start': 11744914}) | ||
|
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||
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| # for v in sample.find({'start': 11744914, 'end': 11748800}): | ||
| # pprint.pprint(v) | ||
|
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||
| #pprint.pprint(sample.find_one()) | ||
| #print(sample.list_collection_names()) | ||
| #if __name__ == "__main__": | ||
| # beacon_query() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,99 @@ | ||
| from pymongo import MongoClient | ||
| import argparse | ||
| import pprint | ||
|
|
||
| def beacon_query(): | ||
| parser = argparse.ArgumentParser(description="Query Beacon Database") | ||
| subparsers = parser.add_subparsers(dest='command') | ||
| subparsers.required = True | ||
|
|
||
| # 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') | ||
|
|
||
| # 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') | ||
|
|
||
| # 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') | ||
|
|
||
| # 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') | ||
|
|
||
| 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}): | ||
| 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}) | ||
|
|
||
|
|
||
| # for v in sample.find({'start': 11744914, 'end': 11748800}): | ||
| # pprint.pprint(v) | ||
|
|
||
| #pprint.pprint(sample.find_one()) | ||
| #print(sample.list_collection_names()) | ||
| #if __name__ == "__main__": | ||
| # beacon_query() |