scan

lightmotif.scan(pssm, sequence, *, threshold=0.0, block_size=256)

Scan a sequence using a fast scanner implementation to identify hits.

See Scanner for more information.

Parameters:

• pssm (ScoringMatrix) – The scoring matrix to use to score the sequence with.

• sequence (StripedSequence) – The striped sequence to process with the scanner. Longer sequences benifit more from the scanning implementation.

• threshold (float) – The score threshold to use for filtering hits. Use ScoringMatrix.score to compute a score threshold from a target p-value. A higher threshold will result in less candidate hits and total runtime.

Returns:

Scanner – The scanner for finding candidate hits in the target sequence.

Raises:

ValueError – When either pssm or sequence are not using the DNA alphabet.

Note

This algorithm is only available for DNA motifs because of implementation requirements.