STAGE 2 OF 5

Clean and validate

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THE BRIEF

Real files are messy: lowercase letters, stray spaces and unexpected characters. A pipeline first cleans each sequence (makes it uppercase and removes all whitespace) and then validates it.

Your task. For each record in a FASTA file, clean its sequence, then decide whether it is VALID: it must be non-empty and contain only the letters A, C, G, T and N (N means "unknown base"). Print the id followed by VALID or INVALID.

Input. A FASTA file (the sequences may contain lowercase letters, spaces and invalid characters).

Output. One line per record: id VALID or id INVALID.

GIVEN INPUT

Your code reads this from standard input (input() or sys.stdin), both here and when it is graded.

>r1
acgtn acgt
>r2
ACGTXACGT
>r3
AC GT
TTGA
>r4
ACG1T
>r5

EXPECTED OUTPUT FOR THIS INPUT

r1 VALID
r2 INVALID
r3 VALID
r4 INVALID
r5 INVALID

SKILLS YOU'LL USE

Stuck? These bank problems practise the same techniques.

Write your code

.ipynb

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Why convert every sequence to uppercase before checking or counting it?

Uppercase letters take less memory So `a` and `A` are treated as the same base instead of being counted or rejected as different symbols Because DNA is always written in capitals in nature It makes the sequence longer

In a DNA sequence, what does the letter N usually mean?

Nucleotide number Nitrogen Any base or an unknown base A stop signal

Explain and submit

Explain why your pipeline cleans a sequence before it validates it, and what would go wrong if the order were reversed.

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