def main():
if os.path.isfile(fa + "_screed"):
from screed import ScreedDB
fadb = ScreedDB(fa)
else:
fadb = screed.read_fasta_sequences(fa)
makeKmerArray(fadb, int(args.ksize), norm)
def load_sequences(path):
'''
Load the sequences and index them if no index has been computed before.
'''
if not Path(path + '_screed').is_file():
print('Indexing sequences ...')
screed.make_db(path)
return ScreedDB(path)
def main():
if os.path.isfile(fa + "_screed"):
from screed import ScreedDB
fadb = ScreedDB(fa)
else:
fadb = screed.read_fasta_sequences(fa)
makeSlices(fadb,maxSlice)
def __init__(self, filepath):
self.sdb = ScreedDB(filepath)
def setup(self):
self.db = ScreedDB(xeno + '_screed')
def setup(self):
self.db = ScreedDB(tri + '_screed')
def setup(self):
self.db = ScreedDB(tests22 + '_screed')
def setup(self):
self.db = ScreedDB(mus + '_screed')
def setup(self):
self.db = ScreedDB(pongo + '_screed')
def setup(self):
self.db = ScreedDB(sorex + '_screed')