def PatternToNumber(Pattern):
l = len(Pattern)
condensed_k_mer_list = condensed_list(l)
index = condensed_k_mer_list.index(Pattern)
return index
def PatternToNumber(Pattern):
l = len(Pattern)
condensed_k_mer_list = condensed_list(l)
index = condensed_k_mer_list.index(Pattern)
return index
def median_string(strings, k):
distance = float("inf") #initialize distance as zero
possibles = condensed_list(k)
median = "none"
for p in possibles:
if string_scores(p, strings) < distance:
distance = string_scores(p, strings)
median = p
return median
def ComputingFrequencies(text, k):
condensed_k_mer_list = condensed_list(k)
janky_seq_counter = {}
for k_mer in condensed_k_mer_list:
count = 0
for i, bp in enumerate(text):
end_index = i+k - 1
# if you haven't gone too far down the pattern (possibility of finding k_mer still exists)
if end_index < len(text):
if k_mer == text[i:i+k]: # checks that k_mer matches pattern
count += 1
janky_seq_counter[k_mer] = count
return janky_seq_counter.values()
def ComputingFrequencies(text, k):
condensed_k_mer_list = condensed_list(k)
janky_seq_counter = {}
for k_mer in condensed_k_mer_list:
count = 0
for i, bp in enumerate(text):
end_index = i + k - 1
# if you haven't gone too far down the pattern (possibility of finding k_mer still exists)
if end_index < len(text):
if k_mer == text[i:i + k]: # checks that k_mer matches pattern
count += 1
janky_seq_counter[k_mer] = count
return janky_seq_counter.values()
def NumberToPattern(index, k):
condensed_k_mer_list = condensed_list(k)
pattern = condensed_k_mer_list[index]
return pattern
def NumberToPattern(index, k):
condensed_k_mer_list = condensed_list(k)
pattern = condensed_k_mer_list[index]
return pattern
