def argument_parser(args):
parser = argparse.ArgumentParser() # pragma: no cover
parser.add_argument(
'-molecular_phenotypes',
action='store_true',
help='List all the molecular_phenotypes') # pragma: no cover
parser.add_argument('-molecular_phenotype',
help='List all the studies for a molecular_phenotype'
) # pragma: no cover
parser.add_argument('-studies',
action='store_true',
help='List all the studies') # pragma: no cover
parser.add_argument(
'-study',
help='Will list \'trait: study\' if it exists') # pragma: no cover
parser.add_argument('-tissues',
action='store_true',
help='List all the tissues') # pragma: no cover
parser.add_argument(
'-tissue',
help='Will list \'study: tissue\' if it exists') # pragma: no cover
parser.add_argument(
'-chromosomes',
action='store_true',
help='Will list all the chromosomes') # pragma: no cover
parser.add_argument('-genes',
action='store_true',
help='List all the genes') # pragma: no cover
properties_handler.set_properties() # pragma: no cover
return parser.parse_args(args) # pragma: no cover
def argument_parser(args):
parser = argparse.ArgumentParser() # pragma: no cover
parser.add_argument('-study',
help='The study to be deleted') # pragma: no cover
properties_handler.set_properties() # pragma: no cover
return parser.parse_args(args) # pragma: no cover
def argument_parser(args):
parser = argparse.ArgumentParser() # pragma: no cover
parser.add_argument(
'-path', help='Full path to the dir where the h5files will be stored'
) # pragma: no cover
parser.add_argument(
'-all',
action='store_true',
help='Use argument if you want to search for all associations'
) # pragma: no cover
parser.add_argument(
'-start',
help='Index of the first association retrieved') # pragma: no cover
parser.add_argument(
'-size', help='Number of retrieved associations') # pragma: no cover
parser.add_argument('-trait',
help='The trait I am looking for') # pragma: no cover
parser.add_argument('-study',
help='The study I am looking for') # pragma: no cover
parser.add_argument('-snp',
help='The SNP I am looking for') # pragma: no cover
parser.add_argument(
'-chr', help='The chromosome I am looking for') # pragma: no cover
parser.add_argument(
'-pval',
help='Filter by pval threshold: -pval floor:ceil') # pragma: no cover
parser.add_argument(
'-bp',
help='Filter with baise pair location threshold: -bp floor:ceil'
) # pragma: no cover
properties_handler.set_properties() # pragma: no cover
return parser.parse_args(args) # pragma: no cover
def register(logger_name):
set_p.set_properties()
properties.LOG_CONF['loggers'][logger_name] = {
'handlers': ['logger'],
'propagate': False
}
LOG_CONF = set_log_path(properties)
logging.config.dictConfig(LOG_CONF)
def argument_parser(args):
parser = argparse.ArgumentParser() # pragma: no cover
parser.add_argument(
'-path', help='Full path to the dir where the h5files will be stored'
) # pragma: no cover
parser.add_argument(
'-all',
action='store_true',
help='Use argument if you want to search for all associations'
) # pragma: no cover
parser.add_argument(
'-start',
help='Index of the first association retrieved') # pragma: no cover
parser.add_argument(
'-size', help='Number of retrieved associations') # pragma: no cover
parser.add_argument('-trait',
help='The trait I am looking for') # pragma: no cover
parser.add_argument('-gene',
help='The gene I am looking for') # pragma: no cover
parser.add_argument('-study',
help='The study I am looking for') # pragma: no cover
parser.add_argument('-tissue',
help='The tissue I am looking for') # pragma: no cover
parser.add_argument(
'-qtl_group',
help='The QTL group/context I am looking for') # pragma: no cover
parser.add_argument('-snp',
help='The SNP I am looking for') # pragma: no cover
parser.add_argument(
'-chr', help='The chromosome I am looking for') # pragma: no cover
parser.add_argument(
'-pval',
help='Filter by pval threshold: -pval floor:ceil') # pragma: no cover
parser.add_argument(
'-bp',
help='Filter with baise pair location threshold: -bp floor:ceil'
) # pragma: no cover
parser.add_argument('-quant_method',
help='The quantification method',
choices=['ge', 'tx', 'txrev', 'microarray', 'exon'],
default='ge',
required=False) # pragma: no cover
parser.add_argument(
'-paginate',
help=
'Sets paginate to "False" if you would like to fetch all associations for your query',
type=au.str2bool,
nargs='?',
const=True,
default=True) # pragma: no cover
properties_handler.set_properties() # pragma: no cover
return parser.parse_args(args) # pragma: no cover
def argument_parser(args):
parser = argparse.ArgumentParser() # pragma: no cover
parser.add_argument('-traits',
action='store_true',
help='List all the traits') # pragma: no cover
parser.add_argument('-studies',
action='store_true',
help='List all the studies') # pragma: no cover
parser.add_argument(
'-study',
help='Will list \'trait: study\' if it exists') # pragma: no cover
properties_handler.set_properties() # pragma: no cover
return parser.parse_args(args) # pragma: no cover
def set_properties():
set_p.set_properties()
def main():
argparser = argparse.ArgumentParser()
argparser.add_argument(
'-f',
help='The path to the summary statistics file to be processed',
required=False)
argparser.add_argument(
'-var',
help='The path to the variant/genotype metadata file',
required=False)
argparser.add_argument(
'-phen',
help='The path to the trait/phenotype metadata file',
required=False)
argparser.add_argument('-expr',
help='The path to the gene expression file',
default=None,
required=False)
argparser.add_argument('-study',
help='The study identifier',
required=False)
argparser.add_argument('-qtl_group',
help='The qtl group e.g. "LCL"',
required=False)
argparser.add_argument('-quant',
help='The quantification method e.g. "gene counts"',
required=False)
argparser.add_argument('-tissue', help='The tissue', required=False)
argparser.add_argument('-chr',
help='The chromosome the data belongs to',
required=False)
argparser.add_argument('-loader',
help='The loader type',
choices=['study', 'trait', 'study_info'],
default=None,
required=True)
argparser.add_argument('-tissue_ont',
help='The tissue ontology term',
required=False)
argparser.add_argument('-treatment', help='The treatment', required=False)
argparser.add_argument('-treatment_ont',
help='The treatment ontology term',
required=False)
argparser.add_argument('-condition_label',
help='The condition label e.g. "naive"',
required=False)
argparser.add_argument(
'-metadata',
help=
'path to tsv containing metadata for the study. Columns "filename", "study", "qtl_group", "tissue_ont", "quant" must be present and will override/replace and of the cmd line arguments given. "filename" refers the basename of the summary statistics file that was passed to the "-f" parameter',
required=False)
args = argparser.parse_args()
properties_handler.set_properties() # pragma: no cover
h5files_path = properties.h5files_path # pragma: no cover
tsvfiles_path = properties.tsvfiles_path # pragma: no cover
database = properties.sqlite_path
chr_dir = properties.chr_dir
trait_dir = properties.trait_dir
study_dir = properties.study_dir
ss_file = args.f
var_file = args.var
phen_file = args.phen
study = args.study
qtl_group = args.qtl_group
quant_method = args.quant
tissue = args.tissue
expr_file = args.expr
loader_type = args.loader
chromosome = args.chr
tissue_ont = args.tissue_ont
treatment = args.treatment
treatment_ont = args.treatment_ont
condition_label = args.condition_label
metadata = args.metadata
if metadata is not None:
study, qtl_group, quant_method, tissue_ont = update_metadate_from_tsv(
metadata, ss_file)
print(study, qtl_group, quant_method, tissue_ont)
if loader_type == 'study':
if chromosome is None:
print("You must specify the '-chr'...exiting")
else:
loader = Loader(tsv=ss_file,
expr_file=expr_file,
var_file=var_file,
qtl_group=qtl_group,
quant_method=quant_method,
study_dir=study_dir,
study=study,
trait=phen_file,
hdf_path=h5files_path,
chromosome=chromosome,
sqldb=database,
loader=loader_type)
#loader = Loader(filename, tsvfiles_path, chr_dir, study_dir, study, traits, h5files_path, chromosome, database, loader_type)
loader.load_bystudy()
elif loader_type == 'trait':
loader = Loader(trait=phen_file,
hdf_path=h5files_path,
loader=loader_type,
trait_dir=trait_dir)
loader.load_traits()
elif loader_type == "study_info":
loader = Loader(qtl_group=qtl_group,
quant_method=quant_method,
study=study,
sqldb=database,
trait=phen_file,
loader=loader_type,
tissue=tissue,
tissue_ont=tissue_ont,
treatment=treatment,
treatment_ont=treatment_ont,
condition_label=condition_label)
#loader = Loader(filename, tsvfiles_path, chr_dir, study_dir, study, traits, h5files_path, chromosome, database, loader_type)
loader.load_study_info()
else:
print("You must specify the '-loader'...exiting")