Question

Write a PYTHON program that tests to see whether a sequence has an AT repeat. For this problem, we’ll define a repeat as 3 or more occurrences of AT, i.e. ATATAT…etc. Read in the sequence from a file (in FASTA format) to test your code.

You can use the attached “Test.txt” sequence.

Return a message to the user whether or not an AT repeat exits in the sequence. Use at least one function.

Test.txt :

>TestSeq
ATGCTTTACGTCTACTGTCGTATGCTTTACGTCTACTGACTGTCGTATGCTTACGTCTACTGTCG
TGCTTTACGTCTACTGACTGTCGTATATATATATATATATTGCTTTACGTCTACTGACTGTCGTA

Answer 1

Below is the complete code as per the requirements. It is well explained inside the code using comments.

# function checks if AT repeat exists
def hasRepeat(line):
    # iterate through all characters of sequence
    for i in range(len(line)-5):
        # check if AT repeat is there
        if line[i:i+6] == 'ATATAT':
            return True
    # if true has not been returned, repeat doesn't exist
    return False
  
# open the file
file = open('Test.txt')

# read all lines in the file
lines = file.read().split("\n")

# variables to keep track of sequence
seqStarted = False
found = 0

# iterate through all lines
for line in lines:
    # break loop if empty line is there
    if len(line) == 0:
        break
    # check if sequence startes
    if seqStarted:
        if line[0] == '>':
            seqStarted = False
            continue
        else:
            # check if sequence has an AT repeat
            if hasRepeat(line):
                # print message and break the loop
                print('AT repeat exists')
                found = 1
                break
    else:      
        # if it is not TestSeq, ignore
        if line != '>TestSeq':
            continue
        else:
            seqStarted = True
            continue

# if not found, print to use
if found == 0:
    print('AT repeat does not exist')

# close the file
file.close()

Below is the screenshot of the code if there is any indentation issue:

Below is the sample output for given sequence:

This completes the requirement. Let me know if you have any queries.

Thanks!