Function scan

Source
pub fn scan<'py>(
    pssm: Bound<'py, ScoringMatrix>,
    sequence: Bound<'py, StripedSequence>,
    threshold: f32,
    block_size: usize,
) -> PyResult<Bound<'py, Scanner>>
Expand description

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

See ~lightmotif.Scanner for more information.

Arguments: pssm (~lightmotif.ScoringMatrix): The scoring matrix to use to score the sequence with. sequence (~lightmotif.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: ~lightmotif.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.