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April 7, 2022 13:30
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(gene-normalization) ~/code/gene-normalization (issue-112) % ipython | |
Python 3.9.12 (main, Mar 26 2022, 15:51:15) | |
Type 'copyright', 'credits' or 'license' for more information | |
IPython 8.2.0 -- An enhanced Interactive Python. Type '?' for help. | |
In [2]: import boto3 | |
In [3]: g = boto3.resource("dynamodb").Table("gene_concepts") | |
In [4]: from boto3.dynamodb.conditions import Key | |
In [7]: g.query(KeyConditionExpression=Key("label_and_type").eq("tpx2##alias")) | |
Out[7]: | |
{'Items': [], | |
'Count': 0, | |
'ScannedCount': 0, | |
'ResponseMetadata': {'RequestId': '28VF2LC1A3MG3KKV2GGEB3GSURVV4KQNSO5AEMVJF66Q9ASUAAJG', | |
'HTTPStatusCode': 200, | |
'HTTPHeaders': {'server': 'Server', | |
'date': 'Thu, 07 Apr 2022 12:11:36 GMT', | |
'content-type': 'application/x-amz-json-1.0', | |
'content-length': '39', | |
'connection': 'keep-alive', | |
'x-amzn-requestid': '28VF2LC1A3MG3KKV2GGEB3GSURVV4KQNSO5AEMVJF66Q9ASUAAJG', | |
'x-amz-crc32': '3413411624'}, | |
'RetryAttempts': 0}} | |
In [8]: g.query(KeyConditionExpression=Key("label_and_type").eq("tpx2##xref")) | |
Out[8]: | |
{'Items': [], | |
'Count': 0, | |
'ScannedCount': 0, | |
'ResponseMetadata': {'RequestId': 'E9QHMLJQCUSUR9J80PHGJQN09BVV4KQNSO5AEMVJF66Q9ASUAAJG', | |
'HTTPStatusCode': 200, | |
'HTTPHeaders': {'server': 'Server', | |
'date': 'Thu, 07 Apr 2022 12:11:41 GMT', | |
'content-type': 'application/x-amz-json-1.0', | |
'content-length': '39', | |
'connection': 'keep-alive', | |
'x-amzn-requestid': 'E9QHMLJQCUSUR9J80PHGJQN09BVV4KQNSO5AEMVJF66Q9ASUAAJG', | |
'x-amz-crc32': '3413411624'}, | |
'RetryAttempts': 0}} | |
In [9]: g.query(KeyConditionExpression=Key("label_and_type").eq("tpx2##symbol")) | |
Out[9]: | |
{'Items': [{'src_name': 'Ensembl', | |
'concept_id': 'ensembl:ensg00000088325', | |
'label_and_type': 'tpx2##symbol', | |
'item_type': 'symbol'}, | |
{'src_name': 'HGNC', | |
'concept_id': 'hgnc:1249', | |
'label_and_type': 'tpx2##symbol', | |
'item_type': 'symbol'}, | |
{'src_name': 'NCBI', | |
'concept_id': 'ncbigene:22974', | |
'label_and_type': 'tpx2##symbol', | |
'item_type': 'symbol'}], | |
'Count': 3, | |
'ScannedCount': 3, | |
'ResponseMetadata': {'RequestId': '65I8FMTPOOKQK1CV6MTBB7JLV7VV4KQNSO5AEMVJF66Q9ASUAAJG', | |
'HTTPStatusCode': 200, | |
'HTTPHeaders': {'server': 'Server', | |
'date': 'Thu, 07 Apr 2022 12:11:55 GMT', | |
'content-type': 'application/x-amz-json-1.0', | |
'content-length': '426', | |
'connection': 'keep-alive', | |
'x-amzn-requestid': '65I8FMTPOOKQK1CV6MTBB7JLV7VV4KQNSO5AEMVJF66Q9ASUAAJG', | |
'x-amz-crc32': '2227394646'}, | |
'RetryAttempts': 0}} | |
In [10]: def query(string): | |
...: return g.query(KeyConditionExpression=Key("label_and_type").eq(string)) | |
...: | |
In [12]: query("ensembl:ensg00000088325##identity") | |
Out[12]: | |
{'Items': [{'locations': [{'sequence_id': 'ga4gh:SQ.-A1QmD_MatoqxvgVxBLZTONHz9-c7nQo', | |
'interval': {'type': 'SequenceInterval', | |
'start': {'type': 'Number', 'value': Decimal('31739270')}, | |
'end': {'type': 'Number', 'value': Decimal('31801805')}}, | |
'_id': 'ga4gh:VSL.QUMWyN4wVps8vwXoNJCmhT_b1Vw4XLK_', | |
'type': 'SequenceLocation'}], | |
'merge_ref': 'hgnc:1249', | |
'xrefs': ['hgnc:1249'], | |
'symbol': 'TPX2', | |
'label': 'TPX2 microtubule nucleation factor', | |
'src_name': 'Ensembl', | |
'concept_id': 'ensembl:ENSG00000088325', | |
'label_and_type': 'ensembl:ensg00000088325##identity', | |
'strand': '+', | |
'item_type': 'identity'}], | |
'Count': 1, | |
'ScannedCount': 1, | |
'ResponseMetadata': {'RequestId': '0A4IOA7NRH97KN15CFPBJF536FVV4KQNSO5AEMVJF66Q9ASUAAJG', | |
'HTTPStatusCode': 200, | |
'HTTPHeaders': {'server': 'Server', | |
'date': 'Thu, 07 Apr 2022 12:12:52 GMT', | |
'content-type': 'application/x-amz-json-1.0', | |
'content-length': '712', | |
'connection': 'keep-alive', | |
'x-amzn-requestid': '0A4IOA7NRH97KN15CFPBJF536FVV4KQNSO5AEMVJF66Q9ASUAAJG', | |
'x-amz-crc32': '1424710172'}, | |
'RetryAttempts': 0}} | |
In [13]: query("ncbigene:22974##identity") | |
Out[13]: | |
{'Items': [{'merge_ref': 'hgnc:1249', | |
'aliases': ['HCA519', | |
'REPP86', | |
'GD:C20orf1', | |
'C20orf2', | |
'HCTP4', | |
'C20orf1', | |
'DIL2', | |
'p100', | |
'FLS353', | |
'DIL-2'], | |
'symbol': 'TPX2', | |
'label': 'TPX2 microtubule nucleation factor', | |
'src_name': 'NCBI', | |
'concept_id': 'ncbigene:22974', | |
'label_and_type': 'ncbigene:22974##identity', | |
'item_type': 'identity', | |
'locations': [{'species_id': 'taxonomy:9606', | |
'interval': {'type': 'CytobandInterval', | |
'start': 'q11.21', | |
'end': 'q11.21'}, | |
'_id': 'ga4gh:VCL.lrZVfHmHSb77QV5ukJ6RM933cuNlRyQT', | |
'type': 'ChromosomeLocation', | |
'chr': '20'}, | |
{'sequence_id': 'ga4gh:SQ.-A1QmD_MatoqxvgVxBLZTONHz9-c7nQo', | |
'interval': {'type': 'SequenceInterval', | |
'start': {'type': 'Number', 'value': Decimal('31739247')}, | |
'end': {'type': 'Number', 'value': Decimal('31801802')}}, | |
'_id': 'ga4gh:VSL.fHZf326JNndK-FvuRT17QetuZphxn-pf', | |
'type': 'SequenceLocation'}], | |
'associated_with': ['omim:605917'], | |
'xrefs': ['ensembl:ENSG00000088325', 'hgnc:1249'], | |
'previous_symbols': ['C20ORF2', 'FLS353'], | |
'strand': '+'}], | |
'Count': 1, | |
'ScannedCount': 1, | |
'ResponseMetadata': {'RequestId': 'KR04GUL8QN5BVJ7ISS2HEFLFMJVV4KQNSO5AEMVJF66Q9ASUAAJG', | |
'HTTPStatusCode': 200, | |
'HTTPHeaders': {'server': 'Server', | |
'date': 'Thu, 07 Apr 2022 12:13:04 GMT', | |
'content-type': 'application/x-amz-json-1.0', | |
'content-length': '1241', | |
'connection': 'keep-alive', | |
'x-amzn-requestid': 'KR04GUL8QN5BVJ7ISS2HEFLFMJVV4KQNSO5AEMVJF66Q9ASUAAJG', | |
'x-amz-crc32': '3921033789'}, | |
'RetryAttempts': 0}} | |
In [14]: query("hgnc:1249##identity") | |
Out[14]: | |
{'Items': [], | |
'Count': 0, | |
'ScannedCount': 0, | |
'ResponseMetadata': {'RequestId': 'EPONTI3B9SMU0FVFAG4N28SSVFVV4KQNSO5AEMVJF66Q9ASUAAJG', | |
'HTTPStatusCode': 200, | |
'HTTPHeaders': {'server': 'Server', | |
'date': 'Thu, 07 Apr 2022 12:13:38 GMT', | |
'content-type': 'application/x-amz-json-1.0', | |
'content-length': '39', | |
'connection': 'keep-alive', | |
'x-amzn-requestid': 'EPONTI3B9SMU0FVFAG4N28SSVFVV4KQNSO5AEMVJF66Q9ASUAAJG', | |
'x-amz-crc32': '3413411624'}, | |
'RetryAttempts': 0}} | |
In [15]: exit() | |
(gene-normalization) ~/code/gene-normalization (issue-112) % ipython | |
Python 3.9.12 (main, Mar 26 2022, 15:51:15) | |
Type 'copyright', 'credits' or 'license' for more information | |
IPython 8.2.0 -- An enhanced Interactive Python. Type '?' for help. | |
In [1]: from boto3.dynamodb.conditions import Key | |
In [2]: import boto3 | |
In [3]: g = boto3.resource("dynamodb").Table("gene_concepts") | |
In [5]: def query(string): | |
...: return g.query(KeyConditionExpression=Key("label_and_type").eq(string)) | |
...: | |
In [6]: query("hgnc:1249##identity") | |
Out[6]: | |
{'Items': [{'merge_ref': 'hgnc:1249', | |
'aliases': ['HCA519', 'p100', 'FLS353', 'DIL-2'], | |
'symbol': 'TPX2', | |
'label': 'TPX2 microtubule nucleation factor', | |
'src_name': 'HGNC', | |
'concept_id': 'hgnc:1249', | |
'label_and_type': 'hgnc:1249##identity', | |
'symbol_status': 'approved', | |
'item_type': 'identity', | |
'locations': [{'species_id': 'taxonomy:9606', | |
'interval': {'type': 'CytobandInterval', | |
'start': 'q11.21', | |
'end': 'q11.21'}, | |
'_id': 'ga4gh:VCL.lrZVfHmHSb77QV5ukJ6RM933cuNlRyQT', | |
'type': 'ChromosomeLocation', | |
'chr': '20'}], | |
'associated_with': ['vega:OTTHUMG00000032190', | |
'omim:605917', | |
'ccds:CCDS13190', | |
'ucsc:uc002wwp.2', | |
'uniprot:Q9ULW0', | |
'refseq:NM_012112', | |
'pubmed:10393424', | |
'pubmed:12177045', | |
'pubmed:9207457', | |
'pubmed:12389033', | |
'ena.embl:AF098158'], | |
'xrefs': ['ncbigene:22974', 'ensembl:ENSG00000088325'], | |
'previous_symbols': ['C20orf2', 'C20orf1']}], | |
'Count': 1, | |
'ScannedCount': 1, | |
'ResponseMetadata': {'RequestId': 'QK1UR22ST3B4TCIDINGJDN40GVVV4KQNSO5AEMVJF66Q9ASUAAJG', | |
'HTTPStatusCode': 200, | |
'HTTPHeaders': {'server': 'Server', | |
'date': 'Thu, 07 Apr 2022 13:29:44 GMT', | |
'content-type': 'application/x-amz-json-1.0', | |
'content-length': '1070', | |
'connection': 'keep-alive', | |
'x-amzn-requestid': 'QK1UR22ST3B4TCIDINGJDN40GVVV4KQNSO5AEMVJF66Q9ASUAAJG', | |
'x-amz-crc32': '3728575485'}, | |
'RetryAttempts': 0}} |
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