def __init__(self, db_path, version, run=run, progress=progress, quiet = False):
if not os.path.exists(db_path):
raise ConfigError, "Database ('%s') does not exist. You must create one first." % db_path
self.quiet = quiet
self.db_type = None
self.db_path = db_path
self.version = version
self.next_available_id = {}
self.splits_info = None
self.contigs_info = None
self.split_length = None
self.genes_are_called = None
self.run = run
self.progress = progress
database = db.DB(self.db_path, version)
self.db_type = database.get_meta_value('db_type')
if self.db_type == 'contigs':
# FIXME: a better design is required. the salient point is, "Table" must serve for both profile db
# and contigs db calls.
self.split_length = database.get_meta_value('split_length')
self.genes_are_called = database.get_meta_value('genes_are_called')
self.contigs_info = database.get_table_as_dict(t.contigs_info_table_name, string_the_key = True)
self.splits_info = database.get_table_as_dict(t.splits_info_table_name)
self.contig_name_to_splits = utils.get_contig_name_to_splits_dict(self.splits_info, self.contigs_info)
self.gene_calls_dict = None
database.disconnect()
def __init__(self, db_path, version, run=run, progress=progress, quiet = False):
if not os.path.exists(db_path):
raise ConfigError, "Database ('%s') does not exist. You must create one first." % db_path
self.quiet = quiet
self.db_type = None
self.db_path = db_path
self.version = version
self.next_available_id = {}
self.splits_info = None
self.contigs_info = None
self.split_length = None
self.run = run
self.progress = progress
database = db.DB(self.db_path, version)
self.db_type = database.get_meta_value('db_type')
if self.db_type == 'contigs':
# FIXME: a better design is required. the salient point is, "Table" must serve for both profile db
# and contigs db calls.
self.split_length = database.get_meta_value('split_length')
self.contigs_info = database.get_table_as_dict(t.contigs_info_table_name, string_the_key = True)
self.splits_info = database.get_table_as_dict(t.splits_info_table_name)
self.contig_name_to_splits = utils.get_contig_name_to_splits_dict(self.splits_info, self.contigs_info)
database.disconnect()
def __init__(self,
db_path,
version,
run=run,
progress=progress,
quiet=False,
simple=False):
if not db_path:
raise ConfigError(
"Table superclass is being initiated without a db path, and it is very\
very concerning :( Anvi'o needs an adult.")
if not os.path.exists(db_path):
raise ConfigError(
"Database ('%s') does not exist. You must create one first." %
db_path)
self.quiet = quiet
self.db_type = None
self.db_path = db_path
self.version = version
self.next_available_id = {}
self.splits_info = None
self.contigs_info = None
self.split_length = None
self.genes_are_called = None
self.run = run
self.progress = progress
database = db.DB(self.db_path, version)
self.db_type = database.get_meta_value('db_type')
if not simple and self.db_type == 'contigs':
# FIXME: a better design is required. the salient point is, "Table" must serve for both profile db
# and contigs db calls.
self.split_length = database.get_meta_value('split_length')
self.genes_are_called = database.get_meta_value('genes_are_called')
self.contigs_info = database.get_table_as_dict(
t.contigs_info_table_name, string_the_key=True)
self.splits_info = database.get_table_as_dict(
t.splits_info_table_name)
self.contig_name_to_splits = utils.get_contig_name_to_splits_dict(
self.splits_info, self.contigs_info)
self.gene_calls_dict = None
database.disconnect()