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)