Dna.filter_variants_consecutive

missionbio.mosaic.dna.Dna.filter_variants_consecutive

Dna.filter_variants_consecutive(proximity: Sequence = (25, 50, 100, 200)) → ndarray

Remove nearby variants.

Remove the variants that are close to each other on the same amplicon. This is likely primer misalignment.

Parameters:

proximitylist-like (int)

If i + 1 variants are less than proximity[i] bases apart, then the variants are removed.

Returns:

keepnp.ndarray

Variants that are to be kept, i.e., variants that are close to each other are discarded.

Examples

for proximity = [25, 50, 100, 250]: - If >1 variants are less than 25 bases apart, remove. - If >2 variants are less than 50 bases apart, remove. - If >3 variants are less than 100 bases apart, remove. - If >4 variants are less than 250 bases apart, remove.