DNA sequencing using python

Question

Using loops, how can I write a function in python, to sort the longest chain of proteins, regardless of order. The function returns a substring that consists only of the character 'A','C','G', and 'T' when ties are mixed up with other elements: Example, in the sequence: 'ACCGXXCXXGTTACTGGGCXTTGT', it returns 'GTTACTGGGC'

Answer 1

If the data is provided as a string you could simply split it by the character 'X' and thereby get a list.

startstring = 'ACCGXXCXXGTTACTGGGCXTTGT'
array = startstring.split('X')

Then looping over the list while checking for the length of the element would give you the right result:

# Initialize placeholders for comparison
temp_max_string = ''
temp_max_length = 0

#Loop over each string in the list
for i in array:
    # Check if the current substring is longer than the longest found so far
    if len(i) > temp_max_length:
        # Replace the placeholders if it is longer
        temp_max_length = len(i)
        temp_max_string = i

print(temp_max_string) # or 'print temp_max_string' if you are using python2.

You could also use the python built-ins to get your result in a more efficient manner:

Sorting by descending length (list.sort())

startstring = 'ACCGXXCXXGTTACTGGGCXTTGT'
array = startstring.split('X')
array.sort(key=len, reverse=True)
print(array[0]) #print the longest since we sorted for descending lengths
print(len(array[0])) # Would give you the length of the longest substring

Only get the longest substring (max()):

startstring = 'ACCGXXCXXGTTACTGGGCXTTGT'
array = startstring.split('X')
longest = max(array, key=len)
print(longest) # gives the longest substring
print(len(longest)) # gives you the length of the longest substring