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.