Validating Sequence Records

Intermediate Python Foundations Python Error Handling Validation Data Quality
Significance:

Real datasets contain malformed records, and a script that crashes on the first bad
line is useless for a file with fifty thousand entries. Defensive validation — checking each record,
reporting what failed and why, and carrying on — is what separates a throwaway script from a tool a lab
can actually rely on. This is the habit that saves you when a collaborator sends a file with three
different problems in it.

Statement

You are given records, one per line, each supposed to contain an identifier and a DNA
sequence separated by a single space.

Validate each record against these rules, checked in this order:

  1. The line must contain exactly two space-separated fields — otherwise the error is MALFORMED.
  2. The sequence must contain only the characters A, C, G, T — otherwise the error is BADCHARS.
  3. The sequence length must be a multiple of 3 — otherwise the error is NOTCODON.

For each valid record print <identifier> OK. For each invalid record print <identifier> <ERROR>,
using the first rule it violates. If a record is MALFORMED and has no usable identifier, use the
literal ? as the identifier.

On the final line print the number of valid records.

Input — read from standard input
Variable Type Description
n
line 1
 int The number of records
1 <= n <= 200
records
line 2..n+1
 str One record per line, identifier and sequence separated by a space
each line 1 to 500 characters

These variables are already read for you in the starter code on the right.

Output

str one verdict line per record, then a final line with the count of valid records

Sample Cases
Sample 1
Input
4
g1 ATGGCC
g2 ATGNCC
g3 ATGG
g4
Expected Output
g1 OK
g2 BADCHARS
g3 NOTCODON
g4 MALFORMED
1
One valid record, then a bad-character record, a non-codon record, and a malformed line.
Sample 2
Input
2
good ACGACG
bad
Expected Output
good OK
bad MALFORMED
1
One passing record and one line with a single field.

Submit also runs your code against 3 hidden test cases. Hidden inputs are never shown — if one fails you'll get its number and a description of the mismatch, not the data.

Constraints
  • Rules are checked in the stated order and only the first failure is reported
  • A line with zero, one, or three or more fields is MALFORMED
  • For a MALFORMED line, use the first field as the identifier if one exists, otherwise ?
  • An empty line counts as a record and is MALFORMED with identifier ?
Further Reading
  • line.split() collapses runs of whitespace, which is what you want for field counting.
  • Use set(seq) <= set("ACGT") to test character validity in a single expression.
  • Check the rules in order and return early on the first failure rather than collecting all errors.
My Notes
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Console output will appear here when you click Run Code or Submit...
Expected: n (int), records (remaining lines)
Next Problem
Count Sequences in a FASTA Stream