Azia - 1 year ago 90

Python Question

I am trying to write code for Approximate Pattern Matching which is as below:

`def HammingDistance(p, q):`

d = 0

for p, q in zip(p, q): # your code here

if p!= q:

d += 1

return d

Pattern = "ATTCTGGA"

Text = "CGCCCGAATCCAGAACGCATTCCCATATTTCGGGACCACTGGCCTCCACGGTACGGACGTCAATCAAAT"

d = 3

def ApproximatePatternMatching(Pattern, Text, d):

positions = [] # initializing list of positions

for i in range(len(Text) - len(Pattern)+1):

if Pattern == Text[i:i+len(Pattern)]:

positions.append(i)# your code here

return positions

print (ApproximatePatternMatching(Pattern, Text, d))

I keep getting the following error:

Failed test #3. You may be failing to account for patterns starting at the first index of text.

Test Dataset:

`GAGCGCTGG`

GAGCGCTGGGTTAACTCGCTACTTCCCGACGAGCGCTGTGGCGCAAATTGGCGATGAAACTGCAGAGAGAACTGGTCATCCAACTGAATTCTCCCCGCTATCGCATTTTGATGCGCGCCGCGTCGATT

2

Your output:

`['[]', '0']`

Correct output:

`['0', '30', '66']`

Can not figure out what I am doing wrong as I am trying to learn python so don't have any idea about programming. Need help?

Answer Source

I'm unsure why you're getting an empty list as one of your outputs - when I run your code above I only get [0] as the print out.

Specifically, your code at present only checks for an exact character substring match, without using the hamming distance definition you also included.

The following should return the result you expect:

```
Pattern = "GAGCGCTGG"
Text = "GAGCGCTGGGTTAACTCGCTACTTCCCGACGAGCGCTGTGGCGCAAATTGGCGATGAAACTGCAGAGAGAACTGGTCATCCAACTGAATTCTCCCCGCTATCGCATTTTGATGCGCGCCGCGTCGATT"
d = 3
def HammingDistance(p, q):
d = 0
for p, q in zip(p, q): # your code here
if p!= q:
d += 1
return d
def ApproximatePatternMatching(Pattern, Text, d):
positions = [] # initializing list of positions
for i in range(len(Text) - len(Pattern)+1):
# and using distance < d, rather than exact matching
if HammingDistance(Pattern, Text[i:i+len(Pattern)]) < d:
positions.append(i)
return positions
print (ApproximatePatternMatching(Pattern, Text, d))
```