#!/usr/local/home/russel/mibi/Software/miniconda2/envs/caspredict_dev/bin/python

import argparse
import os
import sys

from caspredict.xgb import XGB
from caspredict.repeat import RepeatTyper

########## Arguments ##########
ap = argparse.ArgumentParser()

# Required
ap.add_argument('input', help='Input. A simple text file with one repeat sequence per line')

# Optional
ap.add_argument('--kmer', help='kmer size. Has to match training kmer size! [%(default)s].', default=4, type=int)
ap.add_argument('--db', help='Path to database.', default='', type=str)

# Workflow starts here
master = RepeatTyper(ap.parse_args())
xgb = XGB(master)
xgb.predict_repeats()
xgb.print_xgb()
