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#!/usr/bin/env python3
import sys
import py_kmc_api as pka
import argparse
import textwrap
VER = "3.1.1"
DATE = "2019-05-19"
def GeneralHelp():
print('KMC dump ver. {} ({})'.format(VER, DATE))
class VersionHelpAction(argparse.Action):
def __call__(self, parser, namespace, values, option_string=None):
GeneralHelp()
parser.print_help()
parser.exit()
class MyParamsParser(argparse.ArgumentParser):
def error(self, message):
sys.stderr.write('error: %s\n' % message)
GeneralHelp()
self.print_help()
sys.exit(1)
parser = MyParamsParser(add_help=False)
parser.register('action', 'version_help_action', VersionHelpAction)
group1 = parser.add_argument_group('help and version')
group1.add_argument("--version", action='version_help_action', nargs=0, help="print help and version")
group1.add_argument("-h", "--help", action='version_help_action', nargs=0, help="print help and version")
group2 = parser.add_argument_group('normal run')
group2.add_argument("kmc_database", help="kmc database")
group2.add_argument("output_file", help="output file")
group2.add_argument("-ci", "--cutoff_min", type=int, help="exclude k-mers occurring less than CI times", default=0)
group2.add_argument("-cx", "--cutoff_max", type=int, help="exclude k-mers occurring more of than CX times", default=0)
args = parser.parse_args()
kmer_data_base = pka.KMCFile()
if not kmer_data_base.OpenForListing(args.kmc_database):
print("Error: cannot open kmc database")
sys.exit(1)
info = kmer_data_base.Info()
kmer_object = pka.KmerAPI(info.kmer_length)
if args.cutoff_min > 0:
if not kmer_data_base.SetMinCount(args.cutoff_min):
print("Error: cannot set cutoff min")
sys.exit(1)
if args.cutoff_max > 0:
if not kmer_data_base.SetMaxCount(args.cutoff_max):
print("Error: cannot set cutoff max")
sys.exit(1)
output_file = open(args.output_file, 'w')
counter = pka.Count()
while kmer_data_base.ReadNextKmer(kmer_object, counter):
output_file.write("{}\t{}\n".format(kmer_object, counter.value))
output_file.close()
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