config

class integron_finder.config.Config(args)[source]

Config object hold values issue from command lines

__init__(args)[source]

Initialize self. See help(type(self)) for accurate signature.

__weakref__

list of weak references to the object (if defined)

default_topology

The default topology available values are: ‘circ’ for circular or ‘lin’ for linear.

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.

input_dir

The absolute path to the directory where is located the replicon

log_level
Returns:the level to apply to loggers. 0 <= level <=50
Return type:int
model_attc_name

The name of the attc model

model_attc_path

The absolute path to the attC model file

model_dir

The absolute path to the directory containing the models

model_integrase

The absolute path to the integrase model file

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.
model_phage_int

The absolute path to the phage-integrase model file

outdir

The absolute path where to write the results directory

replicon_path

The absolute path to the replicon

result_dir

The absolute path to results directory

tmp_dir(replicon_id)[source]

The absolute path of the tmp results dir.