snapatac2.PyDNAMotifScanner.find#

PyDNAMotifScanner.find(seq, pvalue=1e-05, report_pvalue=False)#

Find motif occurrences in the given sequence above the specified p-value threshold.

Use this method when the positions and scores of forward-strand motif hits are needed. Set report_pvalue=True to also report log10 p-values estimated from the scanner’s score CDF. This method does not scan the reverse complement.

Anti-Patterns#

  • Do NOT use find when reverse-complement hits should be considered; use exist or scan the reverse complement explicitly.

  • Do NOT pass RNA sequences; use DNA letters A/C/G/T.

type seq:

str

param seq:

DNA sequence to scan.

type seq:

str

type pvalue:

float

param pvalue:

P-value threshold for reporting motif occurrences. Default is 1e-5.

type pvalue:

float

type report_pvalue:

bool

param report_pvalue:

Whether to report per-hit log10 p-values. Default is False.

type report_pvalue:

bool

returns:

A list of tuples where each tuple contains the position of the motif occurrence, the natural-log likelihood-ratio score, and optionally the log10 p-value.

rtype:

list[tuple[int, float, float | None]]

Examples

>>> hits = scanner.find("ACGTACGT", pvalue=1e-5, report_pvalue=True)
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