#!/usr/bin/python -u
import os
import argparse
#
if __name__ == '__main__':
#
parser = argparse.ArgumentParser(
description = """
This program will parse the annotations provided by the Ensembl Variant Predictor (VEP)
and create a list of protein consequences which can then be submitted to the
Functional Analysis through Hidden Markov Models (FATHMM) software and server.
""",
epilog = """
Note: in order for this script to work, the VEP must be called using the additional --protein parameter.
""",
)
group = parser.add_argument_group('required arguments')
group.add_argument(
"-i",
dest = "input",
help = "a file containing the VEP annotations to parse",
metavar = "",
default = None,
required = True
)
group.add_argument(
"-o",
dest = "output",
help = "where the protein consequences should be written to",
metavar = "