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bioa.io.amplicon.build_amplicons_from_file

build_amplicons_from_file(filename, se_positions, ref_len)[source]

Creates the Amplicons data structure from a file of reads. The file structure must follow:

read, position

for this to operate correctly.

Parameters :

filename : str

Path to the read-data file.

se_positions : list of (int, int)

List of starting and ending positions for each amplicon.

ref_len : int

Length of the entire reference genome.

Returns :

amplicons : bioa.Amplicons

Amplicon data structure containing all distinct reads and meta-data.