augur.reconstruct_sequences module

Reconstruct alignments from mutations inferred on the tree

augur.reconstruct_sequences.get_sequence(pseq, muts)

reconstruct a child sequence from that of its parent and the mutations

Parameters:

• pseq (str) – sequence of the parent as string, won’t be changed!

• muts (list) – mutations of the type K135T where K is the parental state, 135 is the position in 1-based numbering, and T is the new state

Returns:

reconstructed sequence

Return type:

str

augur.reconstruct_sequences.load_alignments(sequence_files, gene_names)

augur.reconstruct_sequences.register_parser(parent_subparsers)

augur.reconstruct_sequences.run(args)