Python computing_frequenciesの例

コード例 #1

ファイル: better_clump_finding.py プロジェクト: DieterJoubert/coursera_Bioinformatics

def better_clump_finding(genome, k, t, L):
  frequent_patterns = []
  clump = [0] * (4**k)

  text = genome[0:L]
  frequency_array = computing_frequencies(text,k)

  for i in range(0,4**k):
    if frequency_array[i] >= t:
      clump[i] = 1

  for i in range(1,len(genome)-L+1):
    first_pattern = genome[i-1:i-1+k]
    index = pattern_to_number(first_pattern)
    frequency_array[index] = frequency_array[index] - 1
    last_pattern = genome[i+L-k:i+L]
    index = pattern_to_number(last_pattern)
    frequency_array[index] = frequency_array[index] + 1

    if frequency_array[index] >= t:
      clump[index] = 1

  for i in range(0,4**k):
    if clump[i] == 1:
      pattern = number_to_pattern(i,k)
      if pattern not in frequent_patterns:
        frequent_patterns.append(pattern)

  return frequent_patterns

コード例 #2

 def test_computing_frequencies_0(self):
     text = 'ACGCGGCTCTGAAA'
     k = 2
     fr_array = computing_frequencies(text, k)
     a = ' '.join([str(x) for x in fr_array])
     b = '2 1 0 0 0 0 2 2 1 2 1 0 0 1 1 0'
     self.assertEqual(a, b)

コード例 #3

 def test_computing_frequencies_1(self):
     text = 'TGGACACAACGCCACGCAGCGGGAGTTTAGTAATGTCAACAGCTGACGCTCCCTTGATTCAGATGTTGTGCATGGGGTGTCATGGACACAAGACACCTGTGCTGTCCCCACATCGCGTTGTAACTGCAATTTCAGCTTTCGCGTATGGTGCGGTAAACTCGTACAGGGGCTGATTGCCAAACGAAAACGGATGATATATATGCTGTGAGATACTGGGGTGGCAGATACACATGTTGCCTTGATCGGATAGGATTATAGGACAATTTCGTCCATTCATACTTTCTAAGTCGACAGCCATAACATAATGGACGCGGGCAAAACGCTGTCAATGTCATTCATGTAAAGCTGATGAAACGATTGCCCACATTTTAAACCAGCGCTGTTCGGTCTCACATCCACTAGTTCCTATTGTATCGTCGTGAAAGAGTCGCACGCCTTGACTGTGGGCACATCTTCCCTCAGGACAGATCCCAGAAGTCAGAGATTAAGGGGTTCAAAATTTGTGTCAGCAAATTCGTTCACTAAGCTTGGGTTCCGCGCAATGGGCACGTTCGGGGGCCTTGTGGTCGAAATTATTCAGATCTCAATCAGTGGGTTTTCAAG'
     k = 6
     fr_array = computing_frequencies(text, k)
     a = ' '.join([str(x) for x in fr_array])
     b = '0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 2 1 1 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 2 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 2 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 0 0 1 0 0 0 0 0 1 0 0 0 0 1 1 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 1 0 0 1 0 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 1 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0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 1 0 0 0 0 0 1 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0'
     self.assertEqual(a, b)

コード例 #4

ファイル: prob_2994_5.py プロジェクト: DieterJoubert/coursera_Bioinformatics

def prob_2994_5():
  lines = open("data/dataset_2994_5.txt").read().splitlines()

  text = lines[0]
  k = int(lines[1])

  fout = open("out.txt", "w")
  fout.write(" ".join(map(str,computing_frequencies(text,k))))
  fout.close() 

コード例 #5

ファイル: pattern_count.py プロジェクト: kiselevskaya/Bioinformatics

def faster_frequent_words(text, k):
    frequent_patterns = []
    frequency_array = computing_frequencies(text, k)
    max_count = max(frequency_array)
    for i in range(4**k):
        if frequency_array[i] == max_count:
            number = i
            pattern = number_to_pattern(number, k)
            frequent_patterns.append(pattern)
    return frequent_patterns