snapatac2.PyDNAMotif#

class snapatac2.PyDNAMotif(id, pwm)#

Represent a DNA motif as a position weight matrix.

Use this class when a Python workflow needs to scan DNA sequences or test motif enrichment from an explicit PWM. The PWM must have one row per motif position and exactly four columns in A/C/G/T order. Rows are normalized to probabilities during construction.

Anti-Patterns#

Do NOT pass columns in alphabetical ambiguity-code order or any order other than A/C/G/T.
Do NOT pass log-odds scores to pwm; pass nonnegative weights or probabilities that can be normalized row by row.
Do NOT use this object directly for scanning. Create a scanner with with_nucl_prob first.

type id:
param id:: Unique identifier of the motif.
type pwm:
param pwm:: Position weight matrix as a 2D numpy array of shape (length, 4).

See also

read_motifs

Examples

>>> import numpy as np
>>> import snapatac2 as snap
>>> motif = snap.PyDNAMotif(
...     "example",
...     np.array([
...         [0.9, 0.05, 0.03, 0.02],
...         [0.1, 0.8, 0.05, 0.05],
...     ]),
... )
>>> scanner = motif.with_nucl_prob()
>>> scanner.exist("ACGTACGT", pvalue=1e-5)

Attributes

`family`	Return the optional motif family label.
`id`	Return the unique motif identifier.
`name`	Return the optional display name of the motif.

Methods

`info_content`()	Return the information content of the motif.
`with_nucl_prob`([a, c, g, t])	Create a motif scanner with specified nucleotide background probabilities.