Speeding up my code for pset6 DNA in cs50x - python-3.x

Question

I am currently doing CS50 DNA pset and I wrote all of my code but it is slower for large files which results in check50 considering it wrong. I have attached my code and the error check50 shows below.
import sys
import csv
def main():
argc = len(sys.argv)
if (argc != 3):
print("Usage: python dna.py [database] [sequence]")
exit()
# Sets variable name for each argv argument
arg_database = sys.argv[1]
arg_sequence = sys.argv[2]
# Converts sequence csv file to string, and returns as thus
sequence = get_sequence(arg_sequence)
seq_len = len(sequence)
# Returns STR patterns as list
STR_array = return_STRs(arg_database)
STR_array_len = len(STR_array)
# Counts highest instance of consecutively reoccurring STRs
STR_values = STR_count(sequence, seq_len, STR_array, STR_array_len)
DNA_match(STR_values, arg_database, STR_array_len)
# Reads argv2 (sequence), and returns text within as a string
def get_sequence(arg_sequence):
with open(arg_sequence, 'r') as csv_sequence:
sequence = csv_sequence.read()
return sequence
# Reads STR headers from arg1 (database) and returns as list
def return_STRs(arg_database):
with open(arg_database, 'r') as csv_database:
database = csv.reader(csv_database)
STR_array = []
for row in database:
for column in row:
STR_array.append(column)
break
# Removes first column header (name)
del STR_array[0]
return STR_array
def STR_count(sequence, seq_len, STR_array, STR_array_len):
# Creates a list to store max recurrence values for each STR
STR_count_values = [0] * STR_array_len
# Temp value to store current count of STR recurrence
temp_value = 0
# Iterates over each STR in STR_array
for i in range(STR_array_len):
STR_len = len(STR_array[i])
# Iterates over each sequence element
for j in range(seq_len):
# Ensures it's still physically possible for STR to be present in sequence
while (seq_len - j >= STR_len):
# Gets sequence substring of length STR_len, starting from jth element
sub = sequence[j:(j + (STR_len))]
# Compares current substring to current STR
if (sub == STR_array[i]):
temp_value += 1
j += STR_len
else:
# Ensures current STR_count_value is highest
if (temp_value > STR_count_values[i]):
STR_count_values[i] = temp_value
# Resets temp_value to break count, and pushes j forward by 1
temp_value = 0
j += 1
i += 1
return STR_count_values
# Searches database file for DNA matches
def DNA_match(STR_values, arg_database, STR_array_len):
with open(arg_database, 'r') as csv_database:
database = csv.reader(csv_database)
name_array = [] * (STR_array_len + 1)
next(database)
# Iterates over one row of database at a time
for row in database:
name_array.clear()
# Copies entire row into name_array list
for column in row:
name_array.append(column)
# Converts name_array number strings to actual ints
for i in range(STR_array_len):
name_array[i + 1] = int(name_array[i + 1])
# Checks if a row's STR values match the sequence's values, prints the row name if match is found
match = 0
for i in range(0, STR_array_len, + 1):
if (name_array[i + 1] == STR_values[i]):
match += 1
if (match == STR_array_len):
print(name_array[0])
exit()
print("No match")
exit()
main()
Check50 error link:
https://submit.cs50.io/check50/fd890301a0dc9414cd29c2b4dcb27bd47e6d0a48
If you wait for long, then you get the answer but since my program is running slow check50 is considering it wrong

Answer 1

Well, I solved it just by adding a break statement.