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.prettify_alignment(aln)

Converts all bases to uppercase and removes auto reverse-complement prefix (_R_). 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(aln, 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

  • aln (MultipleSeqAlign) – Biopython Alignment

  • 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 – list of trimmed sequences, effectively a multiple alignment

  • Tests

  • —–

  • >>> [s.name for s in strip_non_reference(read_alignment(“tests/data/align/test_aligned_sequences.fasta”), “with_gaps”, keep_reference=False)]

  • Trimmed gaps in with_gaps from the alignment

  • [‘no_gaps’, ‘some_other_seq’, ‘_R_crick_strand’]

  • >>> [s.name for s in strip_non_reference(read_alignment(“tests/data/align/test_aligned_sequences.fasta”), “with_gaps”, keep_reference=True)]

  • Trimmed gaps in with_gaps from the alignment

  • [‘with_gaps’, ‘no_gaps’, ‘some_other_seq’, ‘_R_crick_strand’]

  • >>> [s.name for s in strip_non_reference(read_alignment(“tests/data/align/test_aligned_sequences.fasta”), “no_gaps”, keep_reference=True)]

  • No gaps in alignment to trim (with respect to the reference, no_gaps)

  • [‘with_gaps’, ‘no_gaps’, ‘some_other_seq’, ‘_R_crick_strand’]

  • >>> [s.name for s in strip_non_reference(read_alignment(“tests/data/align/test_aligned_sequences.fasta”), “no_gaps”, keep_reference=False)]

  • No gaps in alignment to trim (with respect to the reference, no_gaps)

  • [‘with_gaps’, ‘some_other_seq’, ‘_R_crick_strand’]

  • >>> [s.name for s in strip_non_reference(read_alignment(“tests/data/align/test_aligned_sequences.fasta”), “missing”, keep_reference=False)]

  • Traceback (most recent call last) – …

  • augur.align.AlignmentError (ERROR: reference missing not found in alignment)

augur.align.write_seqs(seqs, fname)

A wrapper around SeqIO.write with error handling