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%matplotlib inline
import os
import sys
#import pysam
import pandas as pd
#import pybedtools as pybed
import matplotlib as mpl
import matplotlib.pyplot as plt
from __future__ import division

# Libraries just for this problem
import operator
import itertools


    

In [11]:

    

def occurrences(string, sub):
    """ Counts overlapping string occurrences """
    count = start = 0
    while True:
        start = string.find(sub, start) + 1
        if start > 0:
            count += 1
        else:
            return count


    

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def max_dict_by_value(dictionary):
    """Returns top dictionary key and value"""
    return dict(max(dictionary.iteritems(), key=operator.itemgetter(1)))


    

In [38]:

    

def most_frequent_kmer1(seq, kmer_len, num_kmers):
    """ Returns most frequent kmer of length kmer_len
        within a sequence of interest"""
    kmers = dict()
    for i in range(len(seq) - kmer_len + 1):
        kmer = string[i:i+kmer_len]
        if kmer in kmers:
            kmers[kmer] += 1
        else:
            kmers[kmer] = 1
    for i in range(num_kmers):
        maximum = max_dict_by_value(kmers)
        key = maximum.keys()
        kmers.pop(maximum.key(), None)


    

In [38]:

    

def most_frequent_kmer2(seq, kmer_len):
    """ Returns most frequent kmer of length kmer_len
        within a sequence of interest"""
    kmers = dict()
    perms = [''.join(p) for p in itertools.product("ACTG", repeat=kmer_len)]
    for perm in perms:
        kmers[perm] = occurrences(string, perm)


    

In [6]:

    

string = "ACGTTGCATGTCGCATGATGCATGAGAGCT"
kmer_len = 4
kmers = dict()


    

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perms = [''.join(p) for p in permutations('ACTG')]
dictionary = dict()
for perm in perms:
    dictionary[perm] = occurrences(string, perm)


    

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sorted_kmers = sorted(kmers.iteritems(), key=operator.itemgetter(1))


    

    
Out[16]:





1

In [40]:

    

most_frequent_kmer1(string, kmer_len)


    

    
Out[40]:





'CATG'

In [33]:

    

max(kmers, key = lambda x: kmers.get(x))


    

    
Out[33]:





'CATG'

In [34]:

    

maximum = max(kmers.values())
keys = [x for x,y in kmers.items() if y == maximum]


    

In [36]:

    

" ".join(keys)


    

    
Out[36]:





'CATG GCAT'

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