snapatac2.PyDNAMotifScanner

class snapatac2.PyDNAMotifScanner

Scan DNA sequences with a motif-specific scanner.

Use this object to find motif hits, test whether a motif exists in one or more sequences, or construct a motif enrichment test from background sequences. Create it from PyDNAMotif.with_nucl_prob.

Anti-Patterns

• Do NOT instantiate this class directly; create it from a PyDNAMotif.

• Do NOT assume find checks reverse complements. Use exist(..., rc=True) or exists(..., rc=True) when reverse-complement matching is required.

See also

PyDNAMotif.with_nucl_prob

Attributes

id	Return the unique identifier of the scanned motif.
name	Return the optional display name of the scanned motif.

Methods

exist(seq[, pvalue, rc])	Check if the motif exists in the given sequence above the specified p-value threshold.
exists(seqs[, pvalue, rc])	Batch check if the motif exists in the given sequences above the specified p-value threshold.
find(seq[, pvalue, report_pvalue])	Find motif occurrences in the given sequence above the specified p-value threshold.
with_background(seqs[, pvalue])	Create a motif test object using background sequences.