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Clarify default values for inference of ambiguous bases #613

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Aug 27, 2020
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Clarify default values for inference of ambiguous bases #613

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cfc64b7
Add minimal functional tests for augur ancestral
huddlej Aug 26, 2020
1866dc7
Clarify default values for inference of ambiguous bases
huddlej Aug 26, 2020
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13 changes: 9 additions & 4 deletions augur/ancestral.py
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Original file line number Diff line number Diff line change
Expand Up @@ -111,9 +111,9 @@ def register_arguments(parser):
parser.add_argument('--vcf-reference', type=str, help='fasta file of the sequence the VCF was mapped to')
parser.add_argument('--output-vcf', type=str, help='name of output VCF file which will include ancestral seqs')
ambiguous = parser.add_mutually_exclusive_group()
ambiguous.add_argument('--keep-ambiguous', action="store_false", dest='infer_ambiguous',
ambiguous.add_argument('--keep-ambiguous', action="store_true",
help='do not infer nucleotides at ambiguous (N) sites on tip sequences (leave as N).')
ambiguous.add_argument('--infer-ambiguous', action="store_true",
ambiguous.add_argument('--infer-ambiguous', action="store_true", default=True,
help='infer nucleotides at ambiguous (N,W,R,..) sites on tip sequences and replace with most likely state.')
parser.add_argument('--keep-overhangs', action="store_true", default=False,
help='do not infer nucleotides for gaps (-) on either side of the alignment')
Expand Down Expand Up @@ -159,9 +159,14 @@ def run(args):
print("ERROR: this version of augur requires TreeTime 0.7 or later.")
return 1

# Infer ambiguous bases if the user has requested that we infer them (either
# explicitly or by default) and the user has not explicitly requested that
# we keep them.
infer_ambiguous = args.infer_ambiguous and not args.keep_ambiguous

tt = ancestral_sequence_inference(tree=T, aln=aln, ref=ref, marginal=args.inference,
fill_overhangs = not(args.keep_overhangs),
infer_tips = args.infer_ambiguous)
infer_tips = infer_ambiguous)

character_map = {}
for x in tt.gtr.profile_map:
Expand All @@ -173,7 +178,7 @@ def run(args):
character_map[x] = x

anc_seqs['nodes'] = collect_mutations_and_sequences(tt, full_sequences=not is_vcf,
infer_tips=args.infer_ambiguous, character_map=character_map)
infer_tips=infer_ambiguous, character_map=character_map)
# add reference sequence to json structure. This is the sequence with
# respect to which mutations on the tree are defined.
if is_vcf:
Expand Down
58 changes: 58 additions & 0 deletions tests/functional/ancestral.t
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@@ -0,0 +1,58 @@
Integration tests for augur ancestral.

$ pushd "$TESTDIR" > /dev/null
$ export AUGUR="../../bin/augur"

Infer ancestral sequences for the given tree and alignment.
The default is to infer ambiguous bases, so there should not be N bases in the inferred output sequences.

$ ${AUGUR} ancestral \
> --tree ancestral/tree_raw.nwk \
> --alignment ancestral/aligned.fasta \
> --output-node-data "$TMP/ancestral_mutations.json" \
> --output-sequences "$TMP/ancestral_sequences.fasta" > /dev/null
*/treetime/aa_models.py:108: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray (glob)
[0.800038509951648, 1.20274751778601, 1.55207513886163, 1.46600946033173, 0.830022143283238, 1.5416250309563, 1.53255698189437, 1.41208067821187, 1.47469999960758, 0.351200119909572, 0.570542199221932, 1.21378822764856, 0.609532859331199, 0.692733248746636, 1.40887880416009, 1.02015839286433, 0.807404666228614, 1.268589159299, 0.933095433689795]

$ grep N "$TMP/ancestral_sequences.fasta"
>NODE_0000000

Infer ancestral sequences for the given tree and alignment, explicitly requesting that ambiguous bases are inferred.
There should not be N bases in the inferred output sequences.

$ ${AUGUR} ancestral \
> --tree ancestral/tree_raw.nwk \
> --alignment ancestral/aligned.fasta \
> --infer-ambiguous \
> --output-node-data "$TMP/ancestral_mutations.json" \
> --output-sequences "$TMP/ancestral_sequences.fasta" > /dev/null
*/treetime/aa_models.py:108: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray (glob)
[0.800038509951648, 1.20274751778601, 1.55207513886163, 1.46600946033173, 0.830022143283238, 1.5416250309563, 1.53255698189437, 1.41208067821187, 1.47469999960758, 0.351200119909572, 0.570542199221932, 1.21378822764856, 0.609532859331199, 0.692733248746636, 1.40887880416009, 1.02015839286433, 0.807404666228614, 1.268589159299, 0.933095433689795]

$ grep N "$TMP/ancestral_sequences.fasta"
>NODE_0000000

Infer ancestral sequences for the given tree and alignment, explicitly requesting that ambiguous bases are NOT inferred.
There be N bases in the inferred output sequences.

$ ${AUGUR} ancestral \
> --tree ancestral/tree_raw.nwk \
> --alignment ancestral/aligned.fasta \
> --keep-ambiguous \
> --output-node-data "$TMP/ancestral_mutations.json" \
> --output-sequences "$TMP/ancestral_sequences.fasta" > /dev/null
*/treetime/aa_models.py:108: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray (glob)
[0.800038509951648, 1.20274751778601, 1.55207513886163, 1.46600946033173, 0.830022143283238, 1.5416250309563, 1.53255698189437, 1.41208067821187, 1.47469999960758, 0.351200119909572, 0.570542199221932, 1.21378822764856, 0.609532859331199, 0.692733248746636, 1.40887880416009, 1.02015839286433, 0.807404666228614, 1.268589159299, 0.933095433689795]

$ grep N "$TMP/ancestral_sequences.fasta"
>NODE_0000000
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGTATCAACAGGTTTT
AGCTGTGGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGTATCAACAGGTTTT
AGCTGTGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNN

$ popd > /dev/null
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