Download NCBI Pathogen Detection AST and genotype (MicroBIGG-E) data from BigQuery#52
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evolarjun wants to merge 4 commits intoAMRverse:mainfrom
Open
Download NCBI Pathogen Detection AST and genotype (MicroBIGG-E) data from BigQuery#52evolarjun wants to merge 4 commits intoAMRverse:mainfrom
evolarjun wants to merge 4 commits intoAMRverse:mainfrom
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Adds query_ncbi_bq_ast() and query_ncbi_bq_geno() to download data from Google Cloud BigQuery in NCBI browser format. Example script in tests/example_query_ncbi_bq.R
Also converted to two space indentation to match the other code
Also removed some debugging code
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Getting a GCP account and doing the authentication can be a hurdle, but once it's working it's pretty smooth to download AST data and genotype data from GCP.
I included a script
tests/example_query_ncbi_bq.Rthat does an example AMRgen analysis using the data from BigQuery.