def run_query(args):
predicates = get_row_predicates(args)
add_required_columns_to_query(args)
formatter = select_formatter(args)
genotypes_needed = needs_genotypes(args)
gene_needed = needs_gene(args)
try:
subjects = get_subjects(args)
except KeyError:
subjects = []
kwargs = {}
if args.bcolz:
from . import gemini_bcolz
kwargs['variant_id_getter'] = gemini_bcolz.filter
gq = GeminiQuery.GeminiQuery(args.db, out_format=formatter, **kwargs)
gq.run(args.query,
args.gt_filter,
args.show_variant_samples,
args.sample_delim,
predicates,
genotypes_needed,
gene_needed,
args.show_families,
subjects=subjects)
if args.use_header and gq.header:
print(gq.header)
if not args.dgidb:
for row in gq:
print(row)
else:
# collect a list of all the genes that need to be queried
# from DGIdb
genes = defaultdict()
for row in gq:
genes[row['gene']] = True
# collect info from DGIdb
dgidb_info = query_dgidb(genes)
# rerun the query (the cursor is now consumed)
gq = GeminiQuery.GeminiQuery(args.db, out_format=formatter)
gq.run(args.query,
args.gt_filter,
args.show_variant_samples,
args.sample_delim,
predicates,
genotypes_needed,
gene_needed,
args.show_families,
subjects=subjects,
**kwargs)
# report the query results with DGIdb info added at the end.
for row in gq:
print(str(row) + "\t" + str(dgidb_info[row['gene']]))
def family_wise_predicate(args):
formatter = select_formatter(args)
families = get_family_dict(args)
gq = GeminiQuery.GeminiQuery(args.db, out_format=formatter)
predicates = []
for f in families.values():
family_names = [x.name for x in f]
subjects = get_subjects_in_family(args, f).values()
predicates.append(select_subjects_predicate(subjects, args,
family_names))
def predicate(row):
return sum([p(row) for p in predicates]) >= args.min_kindreds
return predicate
def family_wise_predicate(args):
formatter = select_formatter(args)
families = get_family_dict(args)
gq = GeminiQuery.GeminiQuery(args.db, out_format=formatter)
predicates = []
for f in families.values():
family_names = [x.name for x in f]
subjects = get_subjects_in_family(args, f).values()
predicates.append(
select_subjects_predicate(subjects, args, family_names))
def predicate(row):
return sum([p(row) for p in predicates]) >= args.min_kindreds
return predicate
def run_query(args):
predicates = get_row_predicates(args)
add_required_columns_to_query(args)
formatter = select_formatter(args)
genotypes_needed = needs_genotypes(args)
gene_needed = needs_gene(args)
try:
subjects = get_subjects(args)
except KeyError:
subjects = []
kwargs = {}
if args.bcolz:
from . import gemini_bcolz
kwargs['variant_id_getter'] = gemini_bcolz.filter
gq = GeminiQuery.GeminiQuery(args.db, out_format=formatter, **kwargs)
gq.run(args.query, args.gt_filter, args.show_variant_samples,
args.sample_delim, predicates, genotypes_needed,
gene_needed, args.show_families, subjects=subjects)
if args.use_header and gq.header:
print(gq.header)
if not args.dgidb:
for row in gq:
print(row)
else:
# collect a list of all the genes that need to be queried
# from DGIdb
genes = defaultdict()
for row in gq:
genes[row['gene']] = True
# collect info from DGIdb
dgidb_info = query_dgidb(genes)
# rerun the query (the cursor is now consumed)
gq = GeminiQuery.GeminiQuery(args.db, out_format=formatter)
gq.run(args.query, args.gt_filter, args.show_variant_samples,
args.sample_delim, predicates, genotypes_needed,
gene_needed, args.show_families, subjects=subjects, **kwargs)
# report the query results with DGIdb info added at the end.
for row in gq:
print(str(row) + "\t" + str(dgidb_info[row['gene']]))