Scripting with BIGSI

def get_config_from_file(config_file):
    if config_file is None:
        if os.environ.get("BIGSI_CONFIG"):
            config_file = os.environ.get("BIGSI_CONFIG")
        else:
            return DEFAULT_CONFIG
    with open(config_file, "r") as infile:
        config = yaml.load(infile)
    return config
    
### 
config = {
    "storage-engine": "berkeleydb",
    "storage-config": {"filename": "test-berkeleydb"},
    "k": 3, "m": 1000, "h": 3,
} ## or get_config_from_file

from bigsi.graph import BIGSI
bigsi=BIGSI(config)
results=bigsi.search(seq="ATC", threshold=0.9)