bioa.Amplicons.amplicons_from_windows

classmethod Amplicons.amplicons_from_windows(reads, align_start, align_stop, window_sizes, fraction)

Build candidate amplicons from the defined window sizes. Amplicons should be uniformly distributed given a size in the list of allowable sizes.

Parameters :

reads : (str, int)

Tuple of the sequence and aligned starting position.

align_start : int

Where the aligned read set begins in the reference.

align_stop : int

Where the aligned read set ends in the reference.

window_sizes : list

List of allowable amplicon sizes.

fraction : float

The fraction of each size in allowable sizes to try.

Returns :

amplicon_family : list

List of candidate amplicon-sets over the read data.