def run(args):
sb = SciBiomart()
if args.marts: # Check if the user wanted to print the marts
sb.list_marts(True)
return
sb.set_mart(args.m) # Otherwise set the mart
if args.datasets: # Check if the user wanted to print the datasets
sb.list_datasets(True)
return
sb.set_dataset(args.d) # Otherwise set the dataset
if args.filters: # Check if the user wanted to print the filters
sb.list_filters(True)
return
if args.attrs: # Check if the user wanted to print the filters
sb.list_attributes(True)
return
if args.configs:
sb.list_configs(True)
return
# Otherwise they actually have a query so we run it
# Convert the filetrs string to a dict
if args.f:
filters = json.loads(args.f)
else:
filters = None
if args.a:
attrs = args.a.split(",")
else:
attrs = None
if not attrs and args.s: # We need the start and ends at least
attrs = ['external_gene_name', 'chromosome_name', 'start_position', 'end_position', 'strand']
sb.u.dp(['Running query on:',
'\nMart: ', sb.mart,
'\nDataset: ', sb.dataset_version,
'\nFilters: ', filters,
'\nAttributes: ', attrs])
results_df = sb.run_query(filters, attrs)
if args.s == 't': # Check if we need to sort the file
convert_dict = {'start_position': int,
'end_position': int,
'strand': int,
'chromosome_name': str}
sb.u.warn_p(['Removing any genes with no gene name... Required for sorting.'])
results_df = results_df[~results_df['external_gene_name'].isnull()]
results_df = results_df.astype(convert_dict)
results_df = sb.sort_df_on_starts(results_df) # Note the user would have had to select the starts and ends
saved_file = sb.save_as_csv(results_df, args.o)
sb.u.dp(['Saved the output to:', saved_file])
def test_grch37(self):
sb = SciBiomart('http://grch37.ensembl.org/biomart/martservice/')
marts = sb.list_marts()
self.sb = sb
sb.set_mart('ENSEMBL_MART_ENSEMBL')
datasets = sb.list_datasets()
check_datasets_exist = [
'hsapiens_gene_ensembl', 'mmusculus_gene_ensembl'
] # mmusculus_gene_ensembl
found_datasets = []
for d in datasets['name'].values:
if d in check_datasets_exist:
found_datasets.append(d)
def test_list_marts(self):
sb = SciBiomart()
marts = sb.list_marts()
expected_marts = [
'ENSEMBL_MART_ENSEMBL', 'ENSEMBL_MART_MOUSE',
'ENSEMBL_MART_SEQUENCE', 'ENSEMBL_MART_ONTOLOGY',
'ENSEMBL_MART_GENOMIC', 'ENSEMBL_MART_SNP', 'ENSEMBL_MART_FUNCGEN'
]
found_marts = []
# Check that all the marts are in the expected marts list
count_marts = 0
for m in marts:
for mart_attr in m:
if mart_attr == '@name':
assert m[mart_attr] in expected_marts
count_marts += 1
found_marts.append(m[mart_attr])
# Now check we had all of them
print(found_marts)
print(count_marts, len(expected_marts))
assert count_marts == len(expected_marts)
self.sb = sb