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#!/usr/bin/env python3
#
# Copyright (C) 2010 Institute for Computational Biomedicine,
# Weill Medical College of Cornell University
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
import getopt
import os
import stat
import sys
from google.protobuf import text_format
from tensorflow.python.platform.tf_logging import flush
from goby.SequenceBaseInformation import SequenceBaseInformationGenerator
def usage():
print("usage:", sys.argv[0], "[-h|--help] [-v|--verbose] <basename.sbi>")
def main():
verbose = False
try:
opts, args = getopt.getopt(sys.argv[1:], "hv", ["help", "verbose"])
except getopt.GetoptError as err:
print(str(err),file=sys.stderr)
usage()
sys.exit(1)
# Collect options
for opt, arg in opts:
if opt in ("-h", "--help"):
usage()
sys.exit()
elif opt in ("-v", "--verbose"):
verbose = True
if len(args) != 1:
usage()
sys.exit(2)
filename = args[0]
print("sbi filename = %s" % filename)
print()
number_of_entries = 0
records = SequenceBaseInformationGenerator(filename)
for record in records:
number_of_entries += 1
print(record)
if __name__ == "__main__":
main()
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