wspc 0.0.2

Protein-content based pathogenicity classifier

WSPC

Installing the package:

pip install wspc

Dependencies

• Python >=3.6
• Packages: pandas, numpy, sklearn, scipy

Command Line

In windows: make sure that the python "Scripts\" directory is added to PATH, so that the package can be executed as a command

Usage:

usage: wspc [-h] [-m {predict,fit}] -i I [-o OUTPUT] [-l LABELS_PATH] [--model_path MODEL_PATH] [-k K] [-t T]

optional arguments:
  -h, --help            show this help message and exit
  -m {predict,fit}, --mode {predict,fit}
  -i I                  input directory with genome *.txt files or a merged input *.fasta file
  -o OUTPUT, --output OUTPUT
                        output directory, default current directory
  -l LABELS_PATH, --labels_path LABELS_PATH
                        path to *.csv file with labels
  --model_path MODEL_PATH
                        path to a saved model in a *.pkl file. If not provided, saved pre-trained model will be used
  -k K                  parameter for training - selecting k-best features using chi2
  -t T                  parameter for training - clustering threshold

Predict:

wspc -m predict -i path_to_input_genomes

Train:

wspc -m fit -i path_to_input_genomes -l path_to_labels -k 450 -t 0.18