Week 3 Feedback

[dtaylo95]

Python script that performs alignment based on user input

2.25/8

Exercise	Points Possible	Grade
Read in inputs	2	1.5
Initialize matrices	1	0.75
Populate matrices	2	0
Perform traceback	2	0
Write alignment to file	0.5	0
Print out alignment score and number of gaps in each sequence	0.5	0

DNA alignment file

0/0.5

AA alignment file

0/0.5

README.md with alignment score and number of gaps in each sequence for each alignment

0/1

Total: 2.25/10

Great start! There are a few minor issues with what you have so far:

• Make sure that you make your gap penalty a float
  https://github.com/yingshansambi/qbb2023-answers/blob/e3ab5f2fac4b3a698c5e96d32972c7cd703a6bb2/week3/week3homework.py#L10
• When you read in your scoring matrix, you want to make sure you note which column you want to be the index. You also want to specify that the separator should be whitespace
  https://github.com/yingshansambi/qbb2023-answers/blob/e3ab5f2fac4b3a698c5e96d32972c7cd703a6bb2/week3/week3homework.py#L14
• When you initialize your traceback matrix, make sure you're filling in the first row for sequence2 (not the first column)
  https://github.com/yingshansambi/qbb2023-answers/blob/e3ab5f2fac4b3a698c5e96d32972c7cd703a6bb2/week3/week3homework.py#L33-L35

For full credit you still need the following:

• Populate the matrices
• Do traceback
• Write alignment to file
• Print out alignment score and number of gaps in each sequence
• The two alignment files (for DNA and AA)
• README.md with alignment score and number of gaps in each each sequence for each alignment

[dtaylo95]

Regrade 12/6/2023

Almost perfect! I think there's just one minor issue with your traceback. Check your while condition for performing traceback: https://github.com/yingshansambi/qbb2023-answers/blob/faddee313d983474a824c7a6a0d512fed4d1d9dc/week3/week3homework.py#L66

We want to end traceback at the top left (cell [0,0]), but what happens if i or j reaches 0 before the other one does?

Otherwise, this looks great!

Current grade: 9.75/10