def __init__(self,
db=DEFUALT_DB_DIRECTORY,
cachesize=1,
nproc=0,
mode="c"):
self.mode = mode
self.nproc = nproc
self.db = db
try:
self.metadata = self.load_metadata(mode)
except (bsddb3.db.DBNoSuchFileError, bsddb3.db.DBError) as e:
print(e)
if isinstance(e, bsddb3.db.DBError):
raise OSError(
"You don't have permission to access this directory %s ." %
self.db)
else:
raise OSError(
"Cannot find a BIGSI at %s. Run `bigsi init` or BIGSI.create()"
% db)
else:
self.metadata = self.load_metadata(mode=mode)
self.bloom_filter_size = int.from_bytes(
self.metadata['bloom_filter_size'], 'big')
self.num_hashes = int.from_bytes(self.metadata['num_hashes'],
'big')
self.kmer_size = int.from_bytes(self.metadata['kmer_size'], 'big')
self.scorer = Scorer(self.get_num_colours())
self.graph = ProbabilisticBerkeleyDBStorage(
filename=self.graph_filename,
bloom_filter_size=self.bloom_filter_size,
num_hashes=self.num_hashes,
mode=mode)
self.graph.sync()
self.metadata.sync()
def __init__(self, config=None):
if config is None:
config = DEFAULT_CONFIG
self.config = config
self.storage = get_storage(config)
SampleMetadata.__init__(self, self.storage)
KmerSignatureIndex.__init__(self, self.storage)
self.min_unique_kmers_in_query = (
MIN_UNIQUE_KMERS_IN_QUERY
) ## TODO this can be inferred and set at build time
self.scorer=Scorer(self.num_samples)
def test_score():
s = "1111111111111111111111111111111111111111110000000000000000000000000000001111111111111111111111100000000000000000000100000010001111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111110000000000000000000000100000000010001111111111000000000000100000000000000000000000000000000100000000000010000000010000001000000000010000000000000000010001111111100000000000001100010000000000000000000001000000000000110000000000000000000000100000000000000000000100000000000000001010001111111111100000000000000000000100100010011111111111111111100000000001001000001000000000000000000000000000001000000010100000000000000001111111111111111111111111111111111111111111111111111111111111111111111111111111100000010110001000100000000000000000000000000000000000001000001111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111100010000000100000000001010000001111111111111111111111111111111111111111111111111111111111111111100100000000010000000010000000001111111111111111111111111111111111111111111111111111111111111111111111100000100000000000010000000000000010000000011111111000000100010"
scorer = Scorer(5*10**5)
assert scorer.score(s) == {'length': 1174,
'max_mismatches': 269,
'max_nident': 1156,
'max_pident': 98.46678023850085,
'max_score': 1119.98,
'min_mismatches': 18,
'min_nident': 905,
'min_pident': 77.08688245315162,
'min_score': 96.04,
'mismatches': 33,
'nident': 1141,
'pident': 97.18909710391823,
'score': 1064.89,
'evalue': 0.0,
'pvalue': 0.0,
'log_evalue': -1407.74,
'log_pvalue': -1407.74}
def test_score():
s = "1111111111111111111111111111111111111111110000000000000000000000000000001111111111111111111111100000000000000000000100000010001111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111110000000000000000000000100000000010001111111111000000000000100000000000000000000000000000000100000000000010000000010000001000000000010000000000000000010001111111100000000000001100010000000000000000000001000000000000110000000000000000000000100000000000000000000100000000000000001010001111111111100000000000000000000100100010011111111111111111100000000001001000001000000000000000000000000000001000000010100000000000000001111111111111111111111111111111111111111111111111111111111111111111111111111111100000010110001000100000000000000000000000000000000000001000001111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111100010000000100000000001010000001111111111111111111111111111111111111111111111111111111111111111100100000000010000000010000000001111111111111111111111111111111111111111111111111111111111111111111111100000100000000000010000000000000010000000011111111000000100010"
scorer = Scorer(5 * 10**5)
assert scorer.score(s) == {
"length": 1174,
"max_mismatches": 269,
"max_nident": 1156,
"max_pident": 98.46678023850085,
"max_score": 1119.98,
"min_mismatches": 18,
"min_nident": 905,
"min_pident": 77.08688245315162,
"min_score": 96.04,
"mismatches": 33,
"nident": 1141,
"pident": 97.18909710391823,
"score": 1064.89,
"evalue": 0.0,
"pvalue": 0.0,
"log_evalue": -1407.74,
"log_pvalue": -1407.74,
}