def __init__(self,
db,
include_gt_cols=False,
out_format=DefaultRowFormat(None)):
assert os.path.exists(db), "%s does not exist." % db
self.db = db
self.query_executed = False
self.for_browser = False
self.include_gt_cols = include_gt_cols
# try to connect to the provided database
self._connect_to_database()
# extract the column names from the sample table.
# needed for gt-filter wildcard support.
self._collect_sample_table_columns()
# list of samples ids for each clause in the --gt-filter
self.sample_info = collections.defaultdict(list)
# map sample names to indices. e.g. self.sample_to_idx[NA20814] -> 323
self.sample_to_idx = util.map_samples_to_indices(self.c)
# and vice versa. e.g., self.idx_to_sample[323] -> NA20814
self.idx_to_sample = util.map_indices_to_samples(self.c)
self.idx_to_sample_object = util.map_indices_to_sample_objects(self.c)
self.formatter = out_format
self.predicates = [self.formatter.predicate]
def __init__(self, db, include_gt_cols=False,
out_format=DefaultRowFormat(None)):
assert os.path.exists(db), "%s does not exist." % db
self.db = db
self.query_executed = False
self.for_browser = False
self.include_gt_cols = include_gt_cols
# try to connect to the provided database
self._connect_to_database()
# extract the column names from the sample table.
# needed for gt-filter wildcard support.
self._collect_sample_table_columns()
# list of samples ids for each clause in the --gt-filter
self.sample_info = collections.defaultdict(list)
# map sample names to indices. e.g. self.sample_to_idx[NA20814] -> 323
self.sample_to_idx = util.map_samples_to_indices(self.c)
# and vice versa. e.g., self.idx_to_sample[323] -> NA20814
self.idx_to_sample = util.map_indices_to_samples(self.c)
self.idx_to_sample_object = util.map_indices_to_sample_objects(self.c)
self.formatter = out_format
self.predicates = [self.formatter.predicate]
def __init__(self, db, include_gt_cols=False,
out_format=DefaultRowFormat(None)):
assert os.path.exists(db), "%s does not exist." % db
self.db = db
self.query_executed = False
self.for_browser = False
self.include_gt_cols = include_gt_cols
self._connect_to_database()
# map sample names to indices. e.g. self.sample_to_idx[NA20814] -> 323
self.sample_to_idx = util.map_samples_to_indices(self.c)
# and vice versa. e.g., self.idx_to_sample[323] -> NA20814
self.idx_to_sample = util.map_indices_to_samples(self.c)
self.idx_to_sample_object = util.map_indices_to_sample_objects(self.c)
self.formatter = out_format
self.predicates = [self.formatter.predicate]
