def test_get_frequency_map():
with pytest.raises(AssertionError):
get_frequency_map("", 1)
with pytest.raises(AssertionError):
get_frequency_map("GTACGTACC", 0)
with pytest.raises(AssertionError):
get_frequency_map("GTACGTACC", -2)
def find_pattern_clumps(text: str, substring_length: int, window_length: int,
minimum_frequency: int):
"""TODO: [summary]
Returns:
[type]: [description]
"""
patterns = set()
for index in range(len(text) - window_length + 1):
window = text[index:index + window_length]
freq_map = get_frequency_map(text=window,
substring_length=substring_length)
for key, value in freq_map.items():
if value >= minimum_frequency:
patterns.add(key)
return patterns
def find_pattern_clumps(text: str, substring_length: int, window_length: int,
minimum_frequency: int) -> Set[str]:
"""Find patterns forming clumps in a `text`, i.e., returns all the substrings of
length `substring_length` in `text` which occurred at least `minimum_frequency` times
in a window of fixed length `window_length` along the `text`, essentially looking for
a region where a k-mer appears several times in short succession
Returns:
Set[str]: set of strings
"""
patterns = set()
for index in range(len(text) - window_length + 1):
window = text[index:index + window_length]
freq_map = get_frequency_map(text=window,
substring_length=substring_length)
for key, value in freq_map.items():
if value >= minimum_frequency:
patterns.add(key)
return patterns
def find_most_freq_k_substring(text: str,
substring_length: int) -> Tuple[List[str], int]:
"""
Find the most frequent substring of length in a given text
>>> find_most_freq_k_substring("GTACGTACC", 1)
(['C'], 3)
>>> find_most_freq_k_substring("GTACGTACC", 2)
(['GT', 'TA', 'AC'], 2)
>>> find_most_freq_k_substring("GTACGTACC", 4)
(['GTAC'], 2)
>>> find_most_freq_k_substring("GTACGTACC", 6)
(['GTACGT', 'TACGTA', 'ACGTAC', 'CGTACC'], 1)
"""
freq_map = get_frequency_map(text=text, substring_length=substring_length)
frequency = max(freq_map.values())
frequent_substrings = [
key for key, value in freq_map.items() if value == frequency
]
return frequent_substrings, frequency