#!/opt/conda/conda-bld/albatradis_1758427780971/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin/python
import argparse
import sys
import os
import pkg_resources
sys.path.append('../')
sys.path.append('./')
from albatradis.EMBLExpandGenes import EMBLExpandGenes

version = ''
try:
	version = pkg_resources.get_distribution("albatradis").version
except pkg_resources.DistributionNotFound:
	version = 'x.y.z'

parser = argparse.ArgumentParser(
	description = 'Take in an EMBL file and add flanking 3 prime and 5 prime annotation',
	usage = 'albatradis-annotation [options] EMBLfile', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('emblfile', help='Annotation file in EMBL format', type=str)

parser.add_argument('--feature_size',             '-s', help='Feature size', type=int, default=198)
parser.add_argument('--outputfile',                '-o',  help='Output file', type=str, default='output.embl')
parser.add_argument('--verbose',               '-v', action='store_true', help='Print out more information about the analysis while it runs', default = False)
parser.add_argument('--debug', action='store_true', help='Turn on debugging', default = False)
parser.add_argument('--version', action='version', version=str(version))

options = parser.parse_args()

albatradis = EMBLExpandGenes(options.emblfile, options.feature_size)
albatradis.construct_file(options.outputfile)
