devpatelio

def EulerianCycle(strings, format=True):
  ##Ignore this formatting block, it's only for a desired input
    if format:
        graph = [i.split(' -> ') for i in strings]
        graph = dict(graph)
        for (key, val) in graph.items():
            val = val.split(',')
            graph[key] = val

    copy_graph = copy.deepcopy(dict(graph))

devpatelio

lst = ['TCGGGGGTTTTT', 'CCGGTGACTTAC', 'ACGGGGATTTTC', 'TTGGGGACTTTT', 'AAGGGGACTTCC', 'TTGGGGACTTCC', 'TCGGGGATTCAT', 'TCGGGGATTCCT', 'TAGGGGAACTAC', 'TCGGGTATAACC']

formatted = [np.array([i for i in x]) for x in lst]
formatted = np.array([i for i in formatted]).transpose()

counts = Count(formatted, laplace=False)
print(counts.transpose())
entropy = H_e(counts)
# print(entropy)
print(sum(entropy))

devpatelio

def Count(motif_matrix, laplace=True): 
    motif_matrix = list([i for i in motif_matrix])
    N = len(motif_matrix[0]) * 2
    count_matrix = [[] for _ in range(len(motif_matrix))]
    if laplace == True:
        for idx, column in enumerate(motif_matrix):
            count_matrix[idx] = np.asarray([np.asarray((list(column).count(i)+1)/N) for i in ['A', 'C', 'G', 'T']])
    elif laplace == False:
        N = len(motif_matrix[0])
        for idx, column in enumerate(motif_matrix):

devpatelio

def Reconstruction(final, k, d):
    pref = ''.join([i[0] for i in final[:-1]]) + final[-1][:int(len(final[0])/2)]
    suff = ''.join([i[int(len(final[0])/2)] for i in final[:-1]]) + final[-1][int(len(final[0])/2):]

    return pref[:k+d] + suff

txt = _read('dataset_204_16 (2).txt')
params = txt[0].split(' ')
k = int(params[0])
d = int(params[1])

devpatelio

def DeBruijnPair(k, pairs):
    prefs = [str(i[0][:-1]) + str(i[1][:-1]) for i in pairs]
    suffs = [str(i[0][1:]) + str(i[1][1:]) for i in pairs]
    
    pairs = [[prefs[i], suffs[i]] for i in range(len(prefs))]
    pairdebruijn = {key[0]: [] for key in pairs}

    for pair in pairs:
        pairdebruijn[pair[0]].append(pair[1])
    

devpatelio

txt = _read('dataset_203_6.txt')
a = EulerianPath(txt)
print('->'.join(a))

devpatelio

0 -> 1,2422
1 -> 114,3,4,46
10 -> 54,63,705,9
100 -> 101,2785
1000 -> 1002,1110
1001 -> 1000
1002 -> 1247,632
1003 -> 573
1004 -> 1005
1005 -> 1003

devpatelio

def EulerianPath(strings, format=True):
    #Similar formatting for turning txt file to DeBruijn graph in python dict form
    if format:
        graph = [i.split(' -> ') for i in strings]
        graph = dict(graph)
        for (key, val) in graph.items():
            val = val.split(',')
            graph[key] = val
        copy_graph = copy.deepcopy(dict(graph))
    else:

devpatelio

def _read(filename):
    with open(filename, 'r') as sqinput:
        sqinput = sqinput.read().splitlines()
    return sqinput

txt = _read('dataset_203_99 (1).txt')
final = EulerianCycle(txt)
print('->'.join(final))

devpatelio

0 -> 1,19,731
1 -> 290,3,4
10 -> 100,5
100 -> 102,164,269
1000 -> 1002
1001 -> 1185,148
1002 -> 1001
1003 -> 1005
1004 -> 1935,90
1005 -> 1004,2166