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 load_data_to_database(args):
if args.config_file:
conf.read_configuration_file(args.config_file)
elif args.connection_string:
conf.read_configuration_file(DATABASE={'connection_string': args.connection_string})
else:
raise Exception("Either 'config_file' or 'connection_string' must be specified!")
from elaspic import elaspic_database
db = elaspic_database.MyDatabase()
args.data_folder = args.data_folder.rstrip('/')
table_names = args.data_files.split(',') if args.data_files else None
dirpath, dirnames, filenames = next(os.walk(args.data_folder))
for table in elaspic_database.Base.metadata.sorted_tables:
if table_names is not None and table.name not in table_names:
print("Skipping table '{}' because it was not included in the 'table_names' list..."
.format(table.name))
continue
if '{}.tsv'.format(table.name) in filenames:
db.copy_table_to_db(table.name, args.data_folder)
print("Successfully loaded data from file '{}' to table '{}'"
.format('{}.tsv'.format(table.name), table.name))
elif '{}.tsv.gz'.format(table.name) in filenames:
with decompress(os.path.join(args.data_folder, '{}.tsv.gz'.format(table.name))):
db.copy_table_to_db(table.name, args.data_folder.rstrip('/'))
print("Successfully loaded data from file '{}' to table '{}'"
.format('{}.tsv.gz'.format(table.name), table.name))
def elaspic_database(args):
if args.config_file:
conf.read_configuration_file(args.config_file)
elif args.connection_string:
conf.read_configuration_file(DATABASE={'connection_string': args.connection_string})
else:
raise Exception("Either 'config_file' or 'connection_string' must be specified!")
print("Running function '{}'...".format(args.func.__name__))
def delete_database(args):
if args.config_file:
conf.read_configuration_file(args.config_file)
elif args.connection_string:
conf.read_configuration_file(DATABASE={'connection_string': args.connection_string})
else:
raise Exception("Either 'config_file' or 'connection_string' must be specified!")
from elaspic import elaspic_database
db = elaspic_database.MyDatabase()
db.delete_database_tables(args.drop_schema, args.drop_uniprot_sequence)
logger.info('Done!')
def test_sequence_mutation_pipeline(pdb_id_sequence):
unique_temp_dir = op.join(op.splitext(__file__)[0], '.'.join(pdb_id_sequence), '.elaspic')
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)
return helper_fns.run_sequence_mutation_pipeline(pdb_id_sequence, sequence_mutations,)
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)
def elaspic_database_cli(args):
if args.config_file:
conf.read_configuration_file(args.config_file)
elif args.connection_string:
conf.read_configuration_file(
DATABASE={"connection_string": args.connection_string},
LOGGER={"level": LOGGING_LEVELS[args.verbose]},
)
else:
raise Exception("Either 'config_file' or 'connection_string' must be specified!")
tables_basic = [
"domain",
"domain_contact",
"uniprot_sequence",
"provean",
"uniprot_domain",
"uniprot_domain_template",
"uniprot_domain_pair",
"uniprot_domain_pair_template",
]
tables_complete = [
"domain",
"domain_contact",
"uniprot_sequence",
"provean",
"uniprot_domain",
"uniprot_domain_template",
"uniprot_domain_pair",
"uniprot_domain_pair_template",
"uniprot_domain_model",
"uniprot_domain_pair_model",
]
if args.action == "create":
create_database(args)
elif args.action == "load_basic":
load_data_to_database(args, tables_basic)
elif args.action == "load_complete":
load_data_to_database(args, tables_complete)
elif args.action == "delete":
delete_database(args)
else:
raise Exception("Unsupported action: {}".format(args.action))
def elaspic(args):
validate_args(args)
# Read configurations
if args.config_file is not None:
conf.read_configuration_file(args.config_file)
elif args.uniprot_id:
conf.read_configuration_file(
DATABASE={
'connection_string': args.connection_string
},
EXTERNAL_DIRS={
'pdb_dir': args.pdb_dir,
'blast_db_dir': args.blast_db_dir,
'archive_dir': args.archive_dir,
})
elif args.structure_file:
unique_temp_dir = op.abspath(op.join(os.getcwd(), '.elaspic'))
os.makedirs(unique_temp_dir, exist_ok=True)
conf.read_configuration_file(
DEFAULT={
'unique_temp_dir': unique_temp_dir
},
EXTERNAL_DIRS={
'pdb_dir': args.pdb_dir,
'blast_db_dir': args.blast_db_dir,
'archive_dir': args.archive_dir
})
if args.uniprot_id:
# Run database pipeline
if args.uniprot_domain_pair_ids:
logger.debug('uniprot_domain_pair_ids: %s', args.uniprot_domain_pair_ids)
uniprot_domain_pair_ids_asint = (
[int(x) for x in args.uniprot_domain_pair_ids.split(',') if x]
)
else:
uniprot_domain_pair_ids_asint = []
# Run database pipeline
from elaspic import database_pipeline
pipeline = database_pipeline.DatabasePipeline(
args.uniprot_id, args.mutations,
run_type=args.run_type,
uniprot_domain_pair_ids=uniprot_domain_pair_ids_asint
)
pipeline.run()
elif args.structure_file:
# Run local pipeline
from elaspic import standalone_pipeline
pipeline = standalone_pipeline.StandalonePipeline(
args.structure_file, args.sequence_file, args.mutations,
mutation_format=args.mutation_format,
run_type=args.run_type,
)
pipeline.run()
import random
import pytest
import pandas as pd
from elaspic import conf
logger = logging.getLogger(__name__)
# Constants
QUICK = False
CONFIG_FILE = op.join(op.dirname(__file__), 'config_file_database.ini')
if hasattr(pytest, "config"):
QUICK = pytest.config.getoption('--quick')
CONFIG_FILE = pytest.config.getoption('--config-file') or CONFIG_FILE
conf.read_configuration_file(CONFIG_FILE, unique_temp_dir=None)
assert conf.CONFIGS['db_type']
logger.debug('Running quick: {}'.format(QUICK))
logger.debug('Config file: {}'.format(CONFIG_FILE))
# Imports that require a parsed config file
import helper_fns # noqa
from elaspic import elaspic_database # noqa
db = elaspic_database.MyDatabase()
conf.CONFIGS['engine'] = db.get_engine()
conf.CONFIGS['engine'].execute("SET sql_mode = ''")
def elaspic_cli(args):
validate_args(args)
# Read configurations
if args.config_file is not None:
conf.read_configuration_file(args.config_file)
elif args.uniprot_id:
conf.read_configuration_file(
DATABASE={
"connection_string": args.connection_string,
},
EXTERNAL_DIRS={
"pdb_dir": args.pdb_dir,
"blast_db_dir": args.blast_db_dir,
"archive_dir": args.archive_dir,
},
LOGGER={
"level": LOGGING_LEVELS[args.verbose],
},
)
elif args.structure_file:
unique_temp_dir = op.abspath(op.join(os.getcwd(), ".elaspic"))
os.makedirs(unique_temp_dir, exist_ok=True)
conf.read_configuration_file(
DEFAULT={"unique_temp_dir": unique_temp_dir},
EXTERNAL_DIRS={
"pdb_dir": args.pdb_dir,
"blast_db_dir": args.blast_db_dir,
"archive_dir": args.archive_dir,
},
LOGGER={
"level": LOGGING_LEVELS[args.verbose],
},
)
if args.uniprot_id:
# Run database pipeline
if args.uniprot_domain_pair_ids:
logger.debug("uniprot_domain_pair_ids: {}".format(args.uniprot_domain_pair_ids))
uniprot_domain_pair_ids_asint = [
int(x) for x in args.uniprot_domain_pair_ids.split(",") if x
]
else:
uniprot_domain_pair_ids_asint = []
# Run database pipeline
from elaspic import database_pipeline
pipeline = database_pipeline.DatabasePipeline(
args.uniprot_id,
args.mutations,
run_type=args.run_type,
uniprot_domain_pair_ids=uniprot_domain_pair_ids_asint,
)
pipeline.run()
elif args.structure_file:
# Run local pipeline
from elaspic import standalone_pipeline
pipeline = standalone_pipeline.StandalonePipeline(
args.structure_file,
args.sequence_file,
args.mutations,
mutation_format=args.mutation_format,
run_type=args.run_type,
)
pipeline.run()
import pandas as pd
import pytest
from elaspic import conf
logger = logging.getLogger(__name__)
# Constants
QUICK = False
CONFIG_FILE = op.join(op.dirname(__file__), "test_database_pipeline.ini")
if hasattr(pytest, "config"):
QUICK = pytest.config.getoption("--quick")
CONFIG_FILE = pytest.config.getoption("--config-file") or CONFIG_FILE
conf.read_configuration_file(CONFIG_FILE)
assert conf.CONFIGS["db_type"]
logger.debug("Running quick: {}".format(QUICK))
logger.debug("Config file: {}".format(CONFIG_FILE))
# Imports that require a parsed config file
import helper_fns # noqa
from elaspic import elaspic_database # noqa
db = elaspic_database.MyDatabase()
conf.CONFIGS["engine"] = db.get_engine()
conf.CONFIGS["engine"].execute("SET sql_mode = ''")
test_cases = []
