def test_list_filters(self):
sb = SciBiomart()
err = sb.list_filters()
assert err['err'] == MART_SET_ERR
sb.set_mart('ENSEMBL_MART_ENSEMBL')
err = sb.list_filters()
assert err['err'] == DATASET_SET_ERR
sb.set_dataset('fcatus_gene_ensembl')
filters_df = sb.list_filters(False)
assert filters_df['name'].values[0] == 'chromosome_name'
assert filters_df['id'].values[3] == 'seq_region_strand_1020'
self.sb = sb
def test_list_attributes(self):
sb = SciBiomart()
err = sb.list_attributes()
assert err['err'] == MART_SET_ERR
sb.set_mart('ENSEMBL_MART_ENSEMBL')
err = sb.list_attributes()
assert err['err'] == DATASET_SET_ERR
sb.set_dataset('fcatus_gene_ensembl')
df = sb.list_attributes(False)
assert len(df['name'] == 'chromosome_name') > 0
assert 'name_1059' in df[df['name'] == 'chromosome_name']['id'].values
self.sb = sb
def test_set_dataset(self):
sb = SciBiomart()
err = sb.list_configs()
assert err['err'] == MART_SET_ERR
sb.set_mart('ENSEMBL_MART_ENSEMBL')
err = sb.list_configs()
assert err['err'] == DATASET_SET_ERR
sb.set_dataset('hsapiens_gene_ensembl')
assert sb.dataset_version == 'hsapiens_gene_ensembl-GRCh38.p13'
self.sb = sb
def test_run_query(self):
sb = SciBiomart()
err = sb.list_filters()
assert err['err'] == MART_SET_ERR
sb.set_mart('ENSEMBL_MART_ENSEMBL')
err = sb.list_filters()
assert err['err'] == DATASET_SET_ERR
sb.set_dataset('hsapiens_gene_ensembl')
results = sb.run_query(
{'ensembl_gene_id': 'ENSG00000139618,ENSG00000091483'},
['ensembl_gene_id', 'hgnc_symbol', 'uniprotswissprot'])
assert 'ENSG00000139618' in results['ensembl_gene_id'].values
assert 'ENSG00000091483' in results['ensembl_gene_id'].values
assert 'ENSG00000091422' not in results['ensembl_gene_id'].values
assert 'P07954' in results['uniprotswissprot'].values
self.sb = sb
def test_list_configs(self):
sb = SciBiomart()
err = sb.list_configs()
assert err['err'] == MART_SET_ERR
sb.set_mart('ENSEMBL_MART_ENSEMBL')
err = sb.list_configs()
assert err['err'] == DATASET_SET_ERR
sb.set_dataset('fcatus_gene_ensembl')
configs = sb.list_configs(True)
check_configs_exist = ['Exportable', 'Importable', 'MainTable']
found_configs = []
for d in configs:
if d in check_configs_exist:
found_configs.append(d)
print(len(configs))
assert len(found_configs) == len(check_configs_exist)
assert len(configs) == 23
self.sb = sb
def test_human_sequence(self):
sb = SciBiomart()
sb.set_mart('ENSEMBL_MART_ENSEMBL')
sb.set_dataset('hsapiens_gene_ensembl')
attributes = [
'ensembl_gene_id', 'mmusculus_homolog_ensembl_gene',
'mmusculus_homolog_perc_id_r1'
]
results = sb.run_query(
{'ensembl_gene_id': 'ENSG00000139618,ENSG00000091483'}, attributes)
print(results)
self.sb = sb
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
def test_get_gene_flank(self):
sb = SciBiomart()
sb.set_mart('ENSEMBL_MART_ENSEMBL')
sb.set_dataset('hsapiens_gene_ensembl')
attributes = ['ensembl_gene_id', 'gene_flank']
results = sb.run_query(
{
'ensembl_gene_id': 'ENSG00000139618,ENSG00000091483',
'upstream_flank': 500
}, attributes)
print(results)
results.to_csv('results_df.csv', index=False)
self.sb = sb
def test_hg19(self):
sb = SciBiomart()
err = sb.list_datasets()
# Expect an error if we haven't set a mart.
assert err['err'] == MART_SET_ERR
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)
sb.set_dataset('hsapiens_gene_ensembl')
self.sb = sb
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_datasets(self):
sb = SciBiomart()
err = sb.list_datasets()
# Expect an error if we haven't set a mart.
assert err['err'] == MART_SET_ERR
sb.set_mart('ENSEMBL_MART_ENSEMBL')
datasets = sb.list_datasets()
check_datasets_exist = [
'fcatus_gene_ensembl', 'pcoquereli_gene_ensembl',
'lsdomestica_gene_ensembl'
]
found_datasets = []
for d in datasets['name'].values:
if d in check_datasets_exist:
found_datasets.append(d)
print(len(found_datasets), len(check_datasets_exist), len(datasets))
# This has changed over time, probably need to think of a better test
#assert len(found_datasets) == len(check_datasets_exist)
assert len(datasets) > 203
self.sb = sb
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])