I am writing a program that is supposed to return the minimum sequence alignment score (smaller = better), and it worked with the Coursera sample inputs, but for the dataset we're given, I can't manually input the sequences, so I have to resort to using a textfile. There are a few things which I found weird. First things first,
pattern = 'AAA'
DNA = open('practice_data.txt')
empty = []
for lines in DNA:
line=lines.strip().strip('\n')
empty.append(line)
print(empty)
print(smallest_distance(pattern, DNA))
If I run this, my program outputs 0. If I comment out for loop, my program outputs 2. I didn't change DNA, so why should my program behave differently? Also, my strip('\n') is working (and for some reason, strip('n') works just as well) but my strip() is not working. Once I figure this out, I can test out empty in my smallest_distance function.
Here is what my data looks like:
ACTAG
CTTAGTATCACTCTGAAAAGAGATTCCGTATCGATGACCGCCAGTTAATACGTGCGAGAAGTGGACACGGCCGCCGACGGCTTCTACACGCTATTACGATG AACCAACAATTGCTCGAATCCTTCCTCAAAATCGCACACGTCTCTCTGGTCGTAGCACGGATCGGCGACCCACGCGTGACAGCCATCACCTATGATTGCCG
TTAAGGTACTGCTTCATTGATCAACACCCCTCAGCCGGCAATCACTCTGGGTGCGGGCTGGGTTTACAGGGGTATACGGAAACCGCTGCTTGCCCAATAAT
etc...