augur.align module¶
Align multiple sequences from FASTA.
-
exception
augur.align.
AlignmentError
¶ Bases:
Exception
-
augur.align.
check_arguments
(args)¶
-
augur.align.
check_duplicates
(*values)¶
-
augur.align.
ensure_reference_strain_present
(ref_name, existing_alignment, seqs)¶
-
augur.align.
generate_alignment_cmd
(method, nthreads, existing_aln_fname, seqs_to_align_fname, aln_fname, log_fname)¶
-
augur.align.
make_gaps_ambiguous
(aln)¶ replace all gaps by ‘N’ in all sequences in the alignment. TreeTime will treat them as fully ambiguous and replace then with the most likely state. This modifies the alignment in place.
- Parameters
aln (MultipleSeqAlign) – Biopython Alignment
-
augur.align.
prune_seqs_matching_alignment
(seqs, aln)¶ Return a set of seqs excluding those set via exclude & print a warning message for each sequence which is exluded.
-
augur.align.
read_alignment
(fname)¶
-
augur.align.
read_reference
(ref_fname)¶
-
augur.align.
read_sequences
(*fnames)¶
-
augur.align.
register_arguments
(parser)¶
-
augur.align.
run
(args)¶ - Parameters
args (namespace) – arguments passed in via the command-line from augur
- Returns
returns 0 for success, 1 for general error
- Return type
int
-
augur.align.
strip_non_reference
(alignment_fname, reference, keep_reference=False)¶ return sequences that have all insertions relative to the reference removed. The alignment is read from file and returned as list of sequences.
- Parameters
alignment_fname (str) – alignment file name, file needs to be fasta format
reference (str) – name of reference sequence, assumed to be part of the alignment
keep_reference (bool, optional) – by default, the reference sequence is removed after stripping non-reference sequence. To keep the reference, use keep_reference=True
- Returns
list of trimmed sequences, effectively a multiple alignment
- Return type
list
-
augur.align.
write_seqs
(seqs, fname)¶ A wrapper around SeqIO.write with error handling
-
augur.align.
write_uppercase_alignment_in_place
(fname)¶