on="gene_id") extra["pred.perf.pval"] = None extra["pred.perf.qval"] = None extra["pred.perf.R2"] = None extra = extra[[ "gene_id", "gene_name", "gene_type", "n.snps.in.model", "pred.perf.R2", "pred.perf.pval", "pred.perf.qval" ]].rename(columns={ "gene_id": "gene", "gene_name": "genename" }) logging.info("Saving db") Models.create_model_db(args.output, extra, weights) logging.info("Done") if __name__ == "__main__": import argparse parser = argparse.ArgumentParser("Build predition model from data") parser.add_argument("-data_annotation", nargs="+") parser.add_argument("-variant_annotation") parser.add_argument("-model_input") parser.add_argument("--model_filter", nargs="+") parser.add_argument("-output") parser.add_argument("-parsimony", type=int, default=logging.INFO) args = parser.parse_args() Logging.configure_logging(args.parsimony) run(args)
entry[3]) f.write(l.encode()) logging.info("Finished building covariance.") if __name__ == "__main__": import argparse parser = argparse.ArgumentParser( "Build S-MultiXcan covariance from models") parser.add_argument("-parquet_genotype_folder", help="Parquet Genotype folder") parser.add_argument( "-parquet_genotype_pattern", help="Pattern to detect parquet genotypes by chromosome") parser.add_argument("-model_db_folder", help="Folder containing models") parser.add_argument("-model_db_file_pattern", help="Regexp to parse file names") parser.add_argument("-output", help="Where to save stuff") parser.add_argument("--output_rsids", action="store_true") parser.add_argument( "-parsimony", help= "Log verbosity level. 1 is everything being logged. 10 is only high level messages, above 10 will hardly log anything", default="10") args = parser.parse_args() Logging.configure_logging(int(args.parsimony)) run(args)
"-output_column_map", help="Specify multiple key-value pairs to specify format conversion", nargs=2, action="append") parser.add_argument("--insert_value", help="Create a column with a specific value", nargs=2, action="append") parser.add_argument("-output_order", help="Specify output order", nargs='+') parser.add_argument("-output", help="Where the output should go") parser.add_argument("--keep_all_original_entries", action="store_true") parser.add_argument( "-verbosity", help= "Log verbosity level. 1 is everything being logged. 10 is only high level messages, above 10 will hardly log anything", default="10") parser.add_argument( '-meta_extra_col', help= 'Let extra columns in snp_reference_metadata be read. Provide key/value pairs in the format: key1:value1 key2:value2 ...', nargs='+', default=[]) GWASUtilities.add_gwas_arguments_to_parser(parser) args = parser.parse_args() Logging.configure_logging(int(args.verbosity)) run(args)
import argparse parser = argparse.ArgumentParser("Convert gencode file into a table file") parser.add_argument("-gencode_file", help="Where to load file from") parser.add_argument("-output", help="Where to save") parser.add_argument("-gene_type_whitelist", help="Which types of genes to keep", default=[], nargs="+") parser.add_argument("-feature_type_whitelist", help="Which types of genes to keep", default=[], nargs="+") parser.add_argument("-transcript_type_whitelist", help="Which types of transcripts to keep", default=[], nargs="+") parser.add_argument( "-output_column_map", help="Specify multiple key-value pairs to specify format conversion", nargs=2, action="append", default=[]) parser.add_argument("-verbosity", help="Logging verbosity (actually loquacity)", type=int, default=10) args = parser.parse_args() Logging.configure_logging(args.verbosity) run(args)
if __name__ == "__main__": import argparse parser = argparse.ArgumentParser("Run COLOC") parser.add_argument("-parquet_genotype_folder", help="Parquet Genotype file") parser.add_argument("-parquet_genotype_pattern", help="Parquet Genotype file") parser.add_argument("-parquet_genotype_metadata", help="Parquet Genotype variant metadata file") parser.add_argument("-restrict_to_individuals", help="filter to individuals") parser.add_argument("--mode", help="'bhat' or 'z' (z is default)") parser.add_argument("-eqtl", help="Run on a GTEX-like eqtl summary stats file") parser.add_argument("-sample_size", help="number of samples", type=int) parser.add_argument("-cs_output", help="Credible sets.") parser.add_argument("-var_output", help="variables") parser.add_argument( "-parsimony", help= "Log verbosity level. 1 is everything being logged. 10 is only high level messages, above 10 will hardly log anything", default="10") parser.add_argument("-MAX_N", type=int) args = parser.parse_args() Logging.configure_logging(int(args.parsimony), with_date=True) run(args)