Premise:
I am currently working on the following problem:
http://rosalind.info/problems/sseq/
I must find the index combinations of all occurrences of a substring in a string, where the substring is not necessarily contiguous.
My testing parameters:
Main_String = ACGGTTAACGTGACGGTTAAGSSGSSTSSTSSASSA
Substring = GGTTAA
Non-contiguous means that an occurrence of the Substring in the Main_String may look like this:
GGSTTSAASSS where the substring is GGTTAA and the MAIN_STRING - GGSTTSAASSS.
The substring, although cut by random characters (S in our case) is still to be found in the main string. As such, a possible answer would be (format:Letter((index + 1) in Main_String)) G(1)G(2)T(4)T(5)A(7)A(8) = 1, 2, 4, 5, 7, 8. That is easy enough to get for the first match. I need to get all possible variations though, so if we use my testing parameters from above, correct answers would be:
3, 4, 5, 6, 7, 8 and 3, 12, 17, 18, 19, 20 and 3, 15, 17, 18, 19, 20 and so on up to 21, 24, 27, 30, 33, 36.
Question:
I need an algorithm that can provide me with all possible variations of a non-contiguous substring in a given string.
Issue:
This is the code I have so far, which works to an extent, but does not return all possible variations, only some of them.
dna = ''
counter = -1
dna_subseq = ''
dna_subseq_indexes = []
with open('Rosalind_dna.txt', 'r') as file:
data = file.read().split('\n')
for line in data:
if line == '':
continue
if 'Rosalind' in line and counter < 1:
counter += 1
continue
elif 'Rosalind' not in line and counter < 1:
dna += line
elif 'Rosalind' not in line and counter >= 1:
dna_subseq += line
result = 0
dna_subseq_minus_start = dna_subseq[1:]
def find_next(start_parameter, base):
result_func = dna.find(base, start_parameter)
if result_func + 1 in dna_subseq_indexes_subcombo:
if result_func + 1 == 0:
return
find_next(start_parameter + 1, base)
else:
dna_subseq_indexes_subcombo.append(result_func + 1)
return
for index, value in enumerate(dna):
global_start = index
result = 0
while result != -1:
dna_subseq_indexes_subcombo = []
if value == dna_subseq[0]:
dna_subseq_indexes_subcombo.append(index + 1)
Flag = True
for base in dna_subseq_minus_start:
if Flag:
start = global_start
Flag = False
result = dna.find(base, start)
if result + 1 in dna_subseq_indexes_subcombo:
find_next(start + 1, base)
else:
dna_subseq_indexes_subcombo.append(result + 1)
start += 1
dna_subseq_indexes.append(dna_subseq_indexes_subcombo)
global_start += 1
else:
break
final_result = []
for x in dna_subseq_indexes:
test = x.copy()
test.sort()
if test == x:
final_result.append(x)
else:
continue
print(final_result)
I'm not sure your algorithm could find all solutions even if it would be fixed. I tried this logic instead :
Find the initial sequence closest to the left of dna and search all declinations going from right to left recursively. This way the solutions are automatically sorted.
dna = 'ACGGTTAACGTGACGGTTAAGSSGSSTSSTSSASSA'
dna_len = len(dna)
dna_subseq = 'GGTTAA'
subseq_len = len(dna_subseq)
count = 0
print_mode = True # Prints the solutions, set to False to collect them instead
# Finds a single solution starting from the previous one or from a null solution
def find_one_solution(prev_solution, subseq_start, dna_start):
global dna, dna_subseq, subseq_len, count, mode
searched = dna_subseq[subseq_start]
coll = prev_solution[:subseq_start]
subseq_idx = subseq_start
for i in range(dna_start, len(dna), 1):
letter = dna[i]
if letter == searched:
coll.append(i)
subseq_idx += 1
if (subseq_idx == subseq_len): break
else: searched = dna_subseq[subseq_idx]
if len(coll) < subseq_len: return None
count += 1
if (print_mode): print(coll)
return coll
# Recursive function
def find_all_solutions(solutions, solution, subseq_start, limit):
global dna, dna_subseq, subseq_len, print_mode
for start in range(subseq_len-1, limit-1, -1):
# last element
if start == subseq_len-1:
while True:
temp = find_one_solution(solution, start, solution[-1]+1)
if temp == None: break
else: solution = temp
if (not print_mode): solutions.append(solution)
# other elements
else:
# finds the next solution
temp = find_one_solution(solution, start, solution[start]+1)
if temp == None:
continue
else:
solution = temp
if (not print_mode): solutions.append(solution)
# and restarts from end with subseq_start as the left limit
find_all_solutions(solutions, solution, subseq_len-1, start)
def main():
all_solutions = []
# Finds the initial solution
initial_solution = [0] * subseq_len
initial_solution = find_one_solution(initial_solution, 0, initial_solution[0])
if initial_solution == None:
print("No solution found")
else:
if (not print_mode): all_solutions.append(initial_solution)
# Finds all other solutions
find_all_solutions(all_solutions, initial_solution, subseq_len-1, 0)
if (not print_mode): print(all_solutions)
print("Total count:", count)
if __name__=="__main__":
main()
#289 solutions found : [[2, 3, 4, 5, 6, 7], [2, 3, 4, 5, 6, 12], [2, 3, 4, 5, 6, 18], [2, 3, 4, 5, 6, 19], [2, 3, 4, 5, 6, 32], [2, 3, 4, 5, 6, 35], [2, 3, 4, 5, 7, 12], [2, 3, 4, 5, 7, 18], [2, 3, 4, 5, 7, 19], [2, 3, 4, 5, 7, 32], [2, 3, 4, 5, 7, 35], [2, 3, 4, 5, 12, 18], [2, 3, 4, 5, 12, 19], [2, 3, 4, 5, 12, 32], [2, 3, 4, 5, 12, 35], [2, 3, 4, 5, 18, 19], [2, 3, 4, 5, 18, 32], [2, 3, 4, 5, 18, 35], [2, 3, 4, 5, 19, 32], [2, 3, 4, 5, 19, 35], [2, 3, 4, 5, 32, 35], [2, 3, 4, 10, 12, 18], [2, 3, 4, 10, 12, 19], [2, 3, 4, 10, 12, 32], [2, 3, 4, 10, 12, 35], [2, 3, 4, 10, 18, 19], [2, 3, 4, 10, 18, 32], [2, 3, 4, 10, 18, 35], [2, 3, 4, 10, 19, 32], [2, 3, 4, 10, 19, 35], [2, 3, 4, 10, 32, 35], [2, 3, 4, 16, 18, 19], [2, 3, 4, 16, 18, 32], [2, 3, 4, 16, 18, 35], [2, 3, 4, 16, 19, 32], [2, 3, 4, 16, 19, 35], [2, 3, 4, 16, 32, 35], [2, 3, 4, 17, 18, 19], [2, 3, 4, 17, 18, 32], [2, 3, 4, 17, 18, 35], [2, 3, 4, 17, 19, 32], [2, 3, 4, 17, 19, 35], [2, 3, 4, 17, 32, 35], [2, 3, 4, 26, 32, 35], [2, 3, 4, 29, 32, 35], [2, 3, 5, 10, 12, 18], [2, 3, 5, 10, 12, 19], [2, 3, 5, 10, 12, 32], [2, 3, 5, 10, 12, 35], [2, 3, 5, 10, 18, 19], [2, 3, 5, 10, 18, 32], [2, 3, 5, 10, 18, 35], [2, 3, 5, 10, 19, 32], [2, 3, 5, 10, 19, 35], [2, 3, 5, 10, 32, 35], [2, 3, 5, 16, 18, 19], [2, 3, 5, 16, 18, 32], [2, 3, 5, 16, 18, 35], [2, 3, 5, 16, 19, 32], [2, 3, 5, 16, 19, 35], [2, 3, 5, 16, 32, 35], [2, 3, 5, 17, 18, 19], [2, 3, 5, 17, 18, 32], [2, 3, 5, 17, 18, 35], [2, 3, 5, 17, 19, 32], [2, 3, 5, 17, 19, 35], [2, 3, 5, 17, 32, 35], [2, 3, 5, 26, 32, 35], [2, 3, 5, 29, 32, 35], [2, 3, 10, 16, 18, 19], [2, 3, 10, 16, 18, 32], [2, 3, 10, 16, 18, 35], [2, 3, 10, 16, 19, 32], [2, 3, 10, 16, 19, 35], [2, 3, 10, 16, 32, 35], [2, 3, 10, 17, 18, 19], [2, 3, 10, 17, 18, 32], [2, 3, 10, 17, 18, 35], [2, 3, 10, 17, 19, 32], [2, 3, 10, 17, 19, 35], [2, 3, 10, 17, 32, 35], [2, 3, 10, 26, 32, 35], [2, 3, 10, 29, 32, 35], [2, 3, 16, 17, 18, 19], [2, 3, 16, 17, 18, 32], [2, 3, 16, 17, 18, 35], [2, 3, 16, 17, 19, 32], [2, 3, 16, 17, 19, 35], [2, 3, 16, 17, 32, 35], [2, 3, 16, 26, 32, 35], [2, 3, 16, 29, 32, 35], [2, 3, 17, 26, 32, 35], [2, 3, 17, 29, 32, 35], [2, 3, 26, 29, 32, 35], [2, 9, 10, 16, 18, 19], [2, 9, 10, 16, 18, 32], [2, 9, 10, 16, 18, 35], [2, 9, 10, 16, 19, 32], [2, 9, 10, 16, 19, 35], [2, 9, 10, 16, 32, 35], [2, 9, 10, 17, 18, 19], [2, 9, 10, 17, 18, 32], [2, 9, 10, 17, 18, 35], [2, 9, 10, 17, 19, 32], [2, 9, 10, 17, 19, 35], [2, 9, 10, 17, 32, 35], [2, 9, 10, 26, 32, 35], [2, 9, 10, 29, 32, 35], [2, 9, 16, 17, 18, 19], [2, 9, 16, 17, 18, 32], [2, 9, 16, 17, 18, 35], [2, 9, 16, 17, 19, 32], [2, 9, 16, 17, 19, 35], [2, 9, 16, 17, 32, 35], [2, 9, 16, 26, 32, 35], [2, 9, 16, 29, 32, 35], [2, 9, 17, 26, 32, 35], [2, 9, 17, 29, 32, 35], [2, 9, 26, 29, 32, 35], [2, 11, 16, 17, 18, 19], [2, 11, 16, 17, 18, 32], [2, 11, 16, 17, 18, 35], [2, 11, 16, 17, 19, 32], [2, 11, 16, 17, 19, 35], [2, 11, 16, 17, 32, 35], [2, 11, 16, 26, 32, 35], [2, 11, 16, 29, 32, 35], [2, 11, 17, 26, 32, 35], [2, 11, 17, 29, 32, 35], [2, 11, 26, 29, 32, 35], [2, 14, 16, 17, 18, 19], [2, 14, 16, 17, 18, 32], [2, 14, 16, 17, 18, 35], [2, 14, 16, 17, 19, 32], [2, 14, 16, 17, 19, 35], [2, 14, 16, 17, 32, 35], [2, 14, 16, 26, 32, 35], [2, 14, 16, 29, 32, 35], [2, 14, 17, 26, 32, 35], [2, 14, 17, 29, 32, 35], [2, 14, 26, 29, 32, 35], [2, 15, 16, 17, 18, 19], [2, 15, 16, 17, 18, 32], [2, 15, 16, 17, 18, 35], [2, 15, 16, 17, 19, 32], [2, 15, 16, 17, 19, 35], [2, 15, 16, 17, 32, 35], [2, 15, 16, 26, 32, 35], [2, 15, 16, 29, 32, 35], [2, 15, 17, 26, 32, 35], [2, 15, 17, 29, 32, 35], [2, 15, 26, 29, 32, 35], [2, 20, 26, 29, 32, 35], [2, 23, 26, 29, 32, 35], [3, 9, 10, 16, 18, 19], [3, 9, 10, 16, 18, 32], [3, 9, 10, 16, 18, 35], [3, 9, 10, 16, 19, 32], [3, 9, 10, 16, 19, 35], [3, 9, 10, 16, 32, 35], [3, 9, 10, 17, 18, 19], [3, 9, 10, 17, 18, 32], [3, 9, 10, 17, 18, 35], [3, 9, 10, 17, 19, 32], [3, 9, 10, 17, 19, 35], [3, 9, 10, 17, 32, 35], [3, 9, 10, 26, 32, 35], [3, 9, 10, 29, 32, 35], [3, 9, 16, 17, 18, 19], [3, 9, 16, 17, 18, 32], [3, 9, 16, 17, 18, 35], [3, 9, 16, 17, 19, 32], [3, 9, 16, 17, 19, 35], [3, 9, 16, 17, 32, 35], [3, 9, 16, 26, 32, 35], [3, 9, 16, 29, 32, 35], [3, 9, 17, 26, 32, 35], [3, 9, 17, 29, 32, 35], [3, 9, 26, 29, 32, 35], [3, 11, 16, 17, 18, 19], [3, 11, 16, 17, 18, 32], [3, 11, 16, 17, 18, 35], [3, 11, 16, 17, 19, 32], [3, 11, 16, 17, 19, 35], [3, 11, 16, 17, 32, 35], [3, 11, 16, 26, 32, 35], [3, 11, 16, 29, 32, 35], [3, 11, 17, 26, 32, 35], [3, 11, 17, 29, 32, 35], [3, 11, 26, 29, 32, 35], [3, 14, 16, 17, 18, 19], [3, 14, 16, 17, 18, 32], [3, 14, 16, 17, 18, 35], [3, 14, 16, 17, 19, 32], [3, 14, 16, 17, 19, 35], [3, 14, 16, 17, 32, 35], [3, 14, 16, 26, 32, 35], [3, 14, 16, 29, 32, 35], [3, 14, 17, 26, 32, 35], [3, 14, 17, 29, 32, 35], [3, 14, 26, 29, 32, 35], [3, 15, 16, 17, 18, 19], [3, 15, 16, 17, 18, 32], [3, 15, 16, 17, 18, 35], [3, 15, 16, 17, 19, 32], [3, 15, 16, 17, 19, 35], [3, 15, 16, 17, 32, 35], [3, 15, 16, 26, 32, 35], [3, 15, 16, 29, 32, 35], [3, 15, 17, 26, 32, 35], [3, 15, 17, 29, 32, 35], [3, 15, 26, 29, 32, 35], [3, 20, 26, 29, 32, 35], [3, 23, 26, 29, 32, 35], [9, 11, 16, 17, 18, 19], [9, 11, 16, 17, 18, 32], [9, 11, 16, 17, 18, 35], [9, 11, 16, 17, 19, 32], [9, 11, 16, 17, 19, 35], [9, 11, 16, 17, 32, 35], [9, 11, 16, 26, 32, 35], [9, 11, 16, 29, 32, 35], [9, 11, 17, 26, 32, 35], [9, 11, 17, 29, 32, 35], [9, 11, 26, 29, 32, 35], [9, 14, 16, 17, 18, 19], [9, 14, 16, 17, 18, 32], [9, 14, 16, 17, 18, 35], [9, 14, 16, 17, 19, 32], [9, 14, 16, 17, 19, 35], [9, 14, 16, 17, 32, 35], [9, 14, 16, 26, 32, 35], [9, 14, 16, 29, 32, 35], [9, 14, 17, 26, 32, 35], [9, 14, 17, 29, 32, 35], [9, 14, 26, 29, 32, 35], [9, 15, 16, 17, 18, 19], [9, 15, 16, 17, 18, 32], [9, 15, 16, 17, 18, 35], [9, 15, 16, 17, 19, 32], [9, 15, 16, 17, 19, 35], [9, 15, 16, 17, 32, 35], [9, 15, 16, 26, 32, 35], [9, 15, 16, 29, 32, 35], [9, 15, 17, 26, 32, 35], [9, 15, 17, 29, 32, 35], [9, 15, 26, 29, 32, 35], [9, 20, 26, 29, 32, 35], [9, 23, 26, 29, 32, 35], [11, 14, 16, 17, 18, 19], [11, 14, 16, 17, 18, 32], [11, 14, 16, 17, 18, 35], [11, 14, 16, 17, 19, 32], [11, 14, 16, 17, 19, 35], [11, 14, 16, 17, 32, 35], [11, 14, 16, 26, 32, 35], [11, 14, 16, 29, 32, 35], [11, 14, 17, 26, 32, 35], [11, 14, 17, 29, 32, 35], [11, 14, 26, 29, 32, 35], [11, 15, 16, 17, 18, 19], [11, 15, 16, 17, 18, 32], [11, 15, 16, 17, 18, 35], [11, 15, 16, 17, 19, 32], [11, 15, 16, 17, 19, 35], [11, 15, 16, 17, 32, 35], [11, 15, 16, 26, 32, 35], [11, 15, 16, 29, 32, 35], [11, 15, 17, 26, 32, 35], [11, 15, 17, 29, 32, 35], [11, 15, 26, 29, 32, 35], [11, 20, 26, 29, 32, 35], [11, 23, 26, 29, 32, 35], [14, 15, 16, 17, 18, 19], [14, 15, 16, 17, 18, 32], [14, 15, 16, 17, 18, 35], [14, 15, 16, 17, 19, 32], [14, 15, 16, 17, 19, 35], [14, 15, 16, 17, 32, 35], [14, 15, 16, 26, 32, 35], [14, 15, 16, 29, 32, 35], [14, 15, 17, 26, 32, 35], [14, 15, 17, 29, 32, 35], [14, 15, 26, 29, 32, 35], [14, 20, 26, 29, 32, 35], [14, 23, 26, 29, 32, 35], [15, 20, 26, 29, 32, 35], [15, 23, 26, 29, 32, 35], [20, 23, 26, 29, 32, 35]]
To test the validity of the algorithm, I used a simpler sequence from which all the solutions are easy to find manually :
dna = 'AAAAAAAA'
dna_subseq = 'AAAA'
Note that I worked with zero based indices because it's simpler, but you could easily add 1 to all results if you need it.
I would like to try and print Calendar in Matrix format for the whole year using the calendar.monthcalendar function
I'm trying to see if there is a way of incorporating either an if or a while loop so I don't have to run the code 12 times with a different month variable on the end?
So far I ran the below with a different variable to achieve the end result.
print(calendar.monthcalendar(2020,1))
I would like the end result to be a matrix of an entire year like below.
[[0, 0, 1, 2, 3, 4, 5], [6, 7, 8, 9, 10, 11, 12], [13, 14, 15, 16, 17, 18, 19], [20, 21, 22, 23, 24, 25, 26], [27, 28, 29, 30, 31, 0, 0]]
[[0, 0, 0, 0, 0, 1, 2], [3, 4, 5, 6, 7, 8, 9], [10, 11, 12, 13, 14, 15, 16], [17, 18, 19, 20, 21, 22, 23], [24, 25, 26, 27, 28, 29, 0]]
[[0, 0, 0, 0, 0, 0, 1], [2, 3, 4, 5, 6, 7, 8], [9, 10, 11, 12, 13, 14, 15], [16, 17, 18, 19, 20, 21, 22], [23, 24, 25, 26, 27, 28, 29], [30, 31, 0, 0, 0, 0, 0]]
[[0, 0, 1, 2, 3, 4, 5], [6, 7, 8, 9, 10, 11, 12], [13, 14, 15, 16, 17, 18, 19], [20, 21, 22, 23, 24, 25, 26], [27, 28, 29, 30, 0, 0, 0]]
[[0, 0, 0, 0, 1, 2, 3], [4, 5, 6, 7, 8, 9, 10], [11, 12, 13, 14, 15, 16, 17], [18, 19, 20, 21, 22, 23, 24], [25, 26, 27, 28, 29, 30, 31]]
[[1, 2, 3, 4, 5, 6, 7], [8, 9, 10, 11, 12, 13, 14], [15, 16, 17, 18, 19, 20, 21], [22, 23, 24, 25, 26, 27, 28], [29, 30, 0, 0, 0, 0, 0]]
[[0, 0, 1, 2, 3, 4, 5], [6, 7, 8, 9, 10, 11, 12], [13, 14, 15, 16, 17, 18, 19], [20, 21, 22, 23, 24, 25, 26], [27, 28, 29, 30, 31, 0, 0]]
[[0, 0, 0, 0, 0, 1, 2], [3, 4, 5, 6, 7, 8, 9], [10, 11, 12, 13, 14, 15, 16], [17, 18, 19, 20, 21, 22, 23], [24, 25, 26, 27, 28, 29, 30], [31, 0, 0, 0, 0, 0, 0]]
[[0, 1, 2, 3, 4, 5, 6], [7, 8, 9, 10, 11, 12, 13], [14, 15, 16, 17, 18, 19, 20], [21, 22, 23, 24, 25, 26, 27], [28, 29, 30, 0, 0, 0, 0]]
[[0, 0, 0, 1, 2, 3, 4], [5, 6, 7, 8, 9, 10, 11], [12, 13, 14, 15, 16, 17, 18], [19, 20, 21,22, 23, 24, 25], [26, 27, 28, 29, 30, 31, 0]]
[[0, 0, 0, 0, 0, 0, 1], [2, 3, 4, 5, 6, 7, 8], [9, 10, 11, 12, 13, 14, 15], [16, 17, 18, 19, 20, 21, 22], [23, 24, 25, 26, 27, 28, 29], [30, 0, 0, 0, 0, 0, 0]]
[[0, 1, 2, 3, 4, 5, 6], [7, 8, 9, 10, 11, 12, 13], [14, 15, 16, 17, 18, 19, 20], [21, 22, 23, 24, 25, 26, 27], [28, 29, 30, 31, 0, 0, 0]]
You can use a for loop. In each iteration of the loop, the calendar.monthcalendar() function is called. The range() function assigns values to x, from 1 to 12 (13 excluded). Therefore x=1 to x=12 is placed into the calendar.monthcalendar() function 12 times.
for x in range(1,13):
print(calendar.monthcalendar(2020,x))
I would suggest a tutorial, book, or any learning resource because these are the basics of any language you need to grasp before actually starting programming.