Example #1
0
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)
Example #2
0
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)
Example #3
0
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)
Example #4
0
 def __init__(self, filepath):
     self.sdb = ScreedDB(filepath)
Example #5
0
 def setup(self):
     self.db = ScreedDB(xeno + '_screed')
Example #6
0
 def setup(self):
     self.db = ScreedDB(tri + '_screed')
Example #7
0
 def setup(self):
     self.db = ScreedDB(tests22 + '_screed')
Example #8
0
 def setup(self):
     self.db = ScreedDB(mus + '_screed')
Example #9
0
 def setup(self):
     self.db = ScreedDB(pongo + '_screed')
Example #10
0
 def setup(self):
     self.db = ScreedDB(sorex + '_screed')