augur.reconstruct_sequences module¶
Reconstruct alignments from mutations inferred on the tree
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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
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augur.reconstruct_sequences.
load_alignments
(sequence_files, gene_names)¶
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augur.reconstruct_sequences.
register_arguments
(parser)¶
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augur.reconstruct_sequences.
run
(args)¶