import time

import sys

import re

import pdb,math

import os

import os.path

import collections

from collections import defaultdict

from weight_updated_graph import weight_updated_graph

def run_cmd(s1):

print(s1); os.system(s1)

class Counter():

print "{:s}: {:s}, processed {:d}".format(time.asctime(), self.name, self.count)

reverse_complement = lambda x: ''.join([{'A':'T','C':'G','G':'C','T':'A'}[B] for B in x][::-1])

'''def reverse_complement(bases):

replacements = [('A', 't'), ('T', 'a'), ('C', 'g'), ('G', 'c')]

for ch1, ch2 in replacements:

bases = re.sub(ch1, ch2, bases)

return bases[::-1].upper()'''

def kmers_for_component(k1mer_dictionary,kmer_directory, reads_files, directory_name, contig_file_extension, get_partition_k1mers, double_stranded = True, paired_end = False, repartition = False, partition_size = 500, overload = 1.5, K = 24, gpmetis_path = 'gpmetis', penalty = 5, only_reads = False):

return [components_broken, newcomps]