def test_pdb_mutation_pipeline_have_sequences(pdb_id):
"""Make sure that we can copy folders with precalculated Provean score(s).
"""
unique_temp_dir_old = _get_unique_temp_dir(pdb_id)
unique_temp_dir = op.join(op.splitext(__file__)[0], pdb_id + '_have_sequences', '.elaspic')
os.makedirs(unique_temp_dir, exist_ok=True)
try:
shutil.copy2(
op.join(unique_temp_dir_old, 'sequence.json'),
op.join(unique_temp_dir, 'sequence.json'))
shutil.copytree(
op.join(unique_temp_dir_old, 'sequence'),
op.join(unique_temp_dir, 'sequence'))
conf.read_configuration_file(
DEFAULT={
'unique_temp_dir': unique_temp_dir
},
EXTERNAL_DIRS={
'pdb_dir': os.environ['PDB_DIR'],
'blast_db_dir': os.environ['BLAST_DB_DIR'],
'archive_dir': os.environ['ARCHIVE_DIR']
}
)
os.chdir(unique_temp_dir)
helper_fns.run_pdb_mutation_pipeline(
pdb_id, pdb_mutatations, have_sequences=True)
except:
raise
finally:
shutil.rmtree(unique_temp_dir)
def test_pdb_mutation_pipeline(pdb_id):
"""Canonical folder.
"""
unique_temp_dir = _get_unique_temp_dir(pdb_id)
os.makedirs(unique_temp_dir, exist_ok=True)
conf.read_configuration_file(
DEFAULT={
'unique_temp_dir': unique_temp_dir
},
EXTERNAL_DIRS={
'pdb_dir': os.environ['PDB_DIR'],
'blast_db_dir': os.environ['BLAST_DB_DIR'],
'archive_dir': os.environ['ARCHIVE_DIR']
}
)
os.chdir(unique_temp_dir)
helper_fns.run_pdb_mutation_pipeline(pdb_id, pdb_mutatations)