bioa.algorithms.reconstruction.amplicon_frequency_matrix_strategy

amplicon_frequency_matrix_strategy(amplicons, use_chi_sqrd=False, norm=False)

Reconstructs quasispecies from the supplied read matrix.

An amplicon strategy is used to pair reads with one another using a most consistent function.

Parameters :

amplicons : Amplicons

Amplicons data-structure where each amplicon is a list of reads. This will be used to construct the frequency matrix.

use_chi_sqrd : bool (optional, default=False)

Whether to use the chi squared test in selecting a guide or the uniform distribution.

norm : bool (optional, default=False)

Whether or not to normalize read counts to frequencies.

Returns :

quasispecies : dict

Quasispecies spectrum with sequences as keys and frequency as value.