config
- class integron_finder.config.Config(args)[source]
Config object hold values issue from command lines
- __weakref__
list of weak references to the object (if defined)
- property default_topology
The default topology available values are: ‘circ’ for circular or ‘lin’ for linear.
- property func_annot_path
The canonical absolute path to the directory containing file needed for the functional annotation. It does not take in account the argument passed via the command line.
- property input_dir
The absolute path to the directory where is located the replicon
- property input_seq_path
The absolute path to the input file
- property log_level
- Returns
the level to apply to loggers. 0 <= level <=50
- Return type
int
- property model_attc_name
The name of the attc model
- property model_attc_path
The absolute path to the attC model file
- property model_dir
The absolute path to the directory containing the models
- property model_integrase
The absolute path to the integrase model file
- property model_len
- Returns
The length of the attc model (corresponding to CLEN field).
- Raises
IOError if model_attc_path does match an existing file RuntimeError if the file doe not content CLEN field.
- property model_phage_int
The absolute path to the phage-integrase model file
- property outdir
The absolute path where to write the results directory
- property result_dir
The absolute path to results directory