def test_BA_one_pred_method_simple(self):
a = base_script + [
'--blast_in',
self.blast_xml,
'--blast_query',
self.query_double,
'--blast_db',
blast_db,
'--mode',
'simple',
'--blast_regexp',
r'(?<=\|)[A-Z0-9]*\.?\d*$',
'--b_type',
'xml',
'--html',
self.html,
'--json',
self.json,
'--csv',
self.csv,
'--pandas_dump',
self.pandas_dump,
'--prediction_method',
'rnafold',
'--enable_overwrite',
'--threads',
'2',
]
bb = call(a, cwd=root)
self.assertEqual(bb, 0)
# we have two input query sequences so output files will be numbered
t = tab_output_equal(
csvfile=iter2file_name(self.csv, True, 0),
jsonfile=iter2file_name(self.json, True, 0),
pdfile=iter2file_name(self.pandas_dump, True, 0),
)
self.assertTrue(t)
t = tab_output_equal(
csvfile=iter2file_name(self.csv, True, 1),
jsonfile=iter2file_name(self.json, True, 1),
pdfile=iter2file_name(self.pandas_dump, True, 1),
)
self.assertTrue(t)
remove_files_with_try([
iter2file_name(self.csv, True, 0),
iter2file_name(self.json, True, 0),
iter2file_name(self.pandas_dump, True, 0),
iter2file_name(self.html, True, 0),
iter2file_name(self.csv, True, 1),
iter2file_name(self.json, True, 1),
iter2file_name(self.pandas_dump, True, 1),
iter2file_name(self.html, True, 1)
], '')
def test_BA_one_pred_method_locarna(self):
a = base_script + [
'--blast_in',
blast_in,
'--blast_query',
blast_query,
'--blast_db',
blast_db,
'--mode',
'locarna',
'--b_type',
'xml',
'--html',
self.html,
'--json',
self.json,
'--csv',
self.csv,
'--prediction_method',
'rnafold',
'--enable_overwrite',
]
bb = call(a, cwd=root)
self.assertEqual(bb, 0)
t = tab_output_equal(
csvfile=self.csv,
jsonfile=self.json,
)
self.assertTrue(t)
def run(mm):
bb = call(self.cmd + ['--prediction_method', mm], cwd=root)
self.assertEqual(bb, 0)
t = tab_output_equal(
csvfile=self.csv,
jsonfile=self.json,
pdfile=self.pandas_dump,
)
self.assertTrue(t)
def run(mm):
bb = call(self.cmd + ['--prediction_method', mm], cwd=root)
self.assertEqual(bb, 0)
t = tab_output_equal(
csvfile=self.csv,
jsonfile=self.json,
pdfile=self.pandas_dump,
)
self.assertTrue(t)
with open(self.json, 'r') as j:
data = json.load(j)
# check if prediction params are empty
self.assertEqual(data['args']['pred_params'][mm], {})
def test_continuation2(self):
with open(blast_output, 'r') as f, open(self.test_backup_file,
'w') as ff:
data = blastsearchrecomputefromdict(json.load(f))
data.args.blast_in = blast_in
data.args.json = None
data.args.html = test_output_file
data.args.sha1 = self.sha1
data.args.prediction_method += ['centroid']
new_structures = {'rnafold': []}
for h in data.hits:
n = copy(h.extension)
n.letter_annotations['ss0'] = n.letter_annotations['rnafold']
del n.letter_annotations['rnafold']
new_structures['rnafold'].append(n)
json.dump([blastsearchrecompute2dict(data)], ff, indent=2)
out = lunch_with_args(self.args)
self.assertEqual(1, 1)
# test_output
for i in range(len(out)):
out[0].to_csv(self.csv)
j_obj = json.dumps(blastsearchrecompute2dict(out[0]), indent=2)
with open(self.json, 'w') as ff:
ff.write(j_obj)
out[0].write_results_fasta(self.fasta)
out[0].write_results_structures(self.fasta_structures)
t = tab_output_equal(csvfile=self.csv,
jsonfile=self.json,
fastafile=self.fasta,
fastastructures=self.fasta_structures,
ref_seqs_file=os.path.join(
fwd, test_data_dir, 'simple.json'))
self.assertEqual(t, True)
