STAGE 4 OF 5

Trim adapters

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THE BRIEF

During sequencing, short synthetic adapter sequences are attached to the DNA fragments. If a read is shorter than the fragment the machine runs through into the adapter, so the read ends with adapter sequence that is not part of the organism's DNA. Left in, it can mislead alignment and assembly.

Your task. The first line is the adapter sequence. Every following line is one read. For each read, find the first occurrence of the adapter and remove it together with everything after it, keeping only what came before. If the adapter does not occur, the read is unchanged. If nothing is left after trimming, print EMPTY.

Input. An adapter line, then one read per line.

Output. One line per read: the trimmed read, or EMPTY.

GIVEN INPUT

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

AGATCGGAAG
ACGTACGTAGATCGGAAGTTTT
GGGGCCCC
AGATCGGAAGACGT
TTAGATCGGAAGAGATCGGAAG

EXPECTED OUTPUT FOR THIS INPUT

ACGTACGT
GGGGCCCC
EMPTY
TT

SKILLS YOU'LL USE

Stuck? These bank problems practise the same techniques.

Trim Adapter Sequences

Write your code

.ipynb

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What is an adapter sequence?

A mutation found in cancer cells A short synthetic sequence attached to DNA fragments so they can be sequenced The gene that makes a protein A type of quality score

Why must adapters be removed before aligning reads to a genome?

They make reads faster to align They are not part of the genome, so they can stop a read from aligning or cause false matches They change the quality scores They are the same as stop codons

Explain and submit

Explain how your code finds the adapter in a read and why it removes everything after the first match as well as the adapter itself.

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