API Reference¶

PyO3 bindings to lightmotif, a library for fast PWM motif scanning.

The API is similar to the Bio.motifs module from Biopython on purpose.

Sequence¶

`lightmotif.EncodedSequence`	A biological sequence encoded as digits.
`lightmotif.StripedSequence`	An encoded biological sequence stored in a column-major matrix.

`lightmotif.CountMatrix`	A matrix storing the count of a motif letters at each position.
`lightmotif.WeightMatrix`	A matrix storing position-specific odds-ratio for a motif.
`lightmotif.ScoringMatrix`	A matrix storing position-specific odds-ratio for a motif.

A striped matrix storing scores obtained with a scoring matrix.

lightmotif.create(sequences)¶

Create a new motif from an iterable of sequences.

All sequences must have the same length, and must contain only valid DNA symbols (A, T, G, C, or N as a wildcard).

Example

>>> sequences = ["TATAAT", "TATAAA", "TATATT", "TATAAT"]
>>> motif = lightmotif.create(sequences)