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joverlee521 merged 1 commit into from
May 19, 2026
Merged

Update Cram tests #1998

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8 changes: 4 additions & 4 deletions tests/functional/ancestral/cram/default-nucleotide-reconstruction.t
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Expand Up @@ -9,15 +9,15 @@ The default is to infer ambiguous bases, so there should not be N bases in the i
> --tree $TESTDIR/../data/tree.nwk \
> --alignment $TESTDIR/../data/aligned.fasta \
> --seed 314159 \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" \
> --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" &> /dev/null
> --output-node-data "ancestral_mutations.json" \
> --output-sequences "ancestral_sequences.fasta" &> /dev/null

$ grep "^N" "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta"
$ grep "^N" "ancestral_sequences.fasta"
[1]

Check that the reference length was correctly exported as the nuc annotation

$ grep -A 6 'annotations' "$CRAMTMP/$TESTFILE/ancestral_mutations.json"
$ grep -A 6 'annotations' "ancestral_mutations.json"
"annotations": {
"nuc": {
"end": 10769,
Expand Down
62 changes: 31 additions & 31 deletions tests/functional/ancestral/cram/infer-ambiguous-nucleotides.t
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Expand Up @@ -10,10 +10,10 @@ There should not be N bases in the inferred output sequences.
> --alignment $TESTDIR/../data/aligned.fasta \
> --infer-ambiguous \
> --seed 314159 \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" \
> --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" &> /dev/null
> --output-node-data "ancestral_mutations.json" \
> --output-sequences "ancestral_sequences.fasta" &> /dev/null

$ grep "^N" "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta"
$ grep "^N" "ancestral_sequences.fasta"
[1]

test ambiguous bases remain in seqs and muts if we use `--keep-ambiguous`
Expand All @@ -32,16 +32,16 @@ and also remain in the resulting sequence.
$ ${AUGUR} ancestral --seed 0 \
> --keep-ambiguous \
> --tree $TESTDIR/../data/simple-genome/tree.nwk --alignment aln_pos3Y.fasta \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations_1.json" \
> --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences_1.fasta" &> /dev/null
> --output-node-data "ancestral_mutations_1.json" \
> --output-sequences "ancestral_sequences_1.fasta" &> /dev/null

$ cat "$CRAMTMP/$TESTFILE/ancestral_mutations_1.json" | jq -c '.nodes.sample_C.muts'
$ cat "ancestral_mutations_1.json" | jq -c '.nodes.sample_C.muts'
["C3Y"]

$ cat "$CRAMTMP/$TESTFILE/ancestral_mutations_1.json" | jq -c '.nodes.sample_C.sequence'
$ cat "ancestral_mutations_1.json" | jq -c '.nodes.sample_C.sequence'
"AAYAA"

$ grep 'sample_C' -A 1 "$CRAMTMP/$TESTFILE/ancestral_sequences_1.fasta"
$ grep 'sample_C' -A 1 "ancestral_sequences_1.fasta"
>sample_C
AAYAA

Expand All @@ -51,16 +51,16 @@ Same test as above but using `--infer-ambiguous` (the default) infers Y as eithe
$ ${AUGUR} ancestral --seed 0 \
> --infer-ambiguous \
> --tree $TESTDIR/../data/simple-genome/tree.nwk --alignment aln_pos3Y.fasta \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations_2.json" \
> --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences_2.fasta" &> /dev/null
> --output-node-data "ancestral_mutations_2.json" \
> --output-sequences "ancestral_sequences_2.fasta" &> /dev/null

$ cat "$CRAMTMP/$TESTFILE/ancestral_mutations_2.json" | jq -c '.nodes.sample_C.muts'
$ cat "ancestral_mutations_2.json" | jq -c '.nodes.sample_C.muts'
[]

$ cat "$CRAMTMP/$TESTFILE/ancestral_mutations_2.json" | jq -c '.nodes.sample_C.sequence'
$ cat "ancestral_mutations_2.json" | jq -c '.nodes.sample_C.sequence'
"AACAA"

$ grep 'sample_C' -A 1 "$CRAMTMP/$TESTFILE/ancestral_sequences_2.fasta"
$ grep 'sample_C' -A 1 "ancestral_sequences_2.fasta"
>sample_C
AACAA

Expand All @@ -83,17 +83,17 @@ and reported in both sequences and mutations. Note that the parent state
$ ${AUGUR} ancestral --seed 0 \
> --keep-ambiguous \
> --tree $TESTDIR/../data/simple-genome/tree.nwk --alignment aln_pos3X.fasta \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations_3.json" \
> --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences_3.fasta" &> /dev/null
> --output-node-data "ancestral_mutations_3.json" \
> --output-sequences "ancestral_sequences_3.fasta" &> /dev/null


$ cat "$CRAMTMP/$TESTFILE/ancestral_mutations_3.json" | jq -c '.nodes.sample_C.muts'
$ cat "ancestral_mutations_3.json" | jq -c '.nodes.sample_C.muts'
["G3N"]

$ cat "$CRAMTMP/$TESTFILE/ancestral_mutations_3.json" | jq -c '.nodes.sample_C.sequence'
$ cat "ancestral_mutations_3.json" | jq -c '.nodes.sample_C.sequence'
"AANAA"

$ grep 'sample_C' -A 1 "$CRAMTMP/$TESTFILE/ancestral_sequences_3.fasta"
$ grep 'sample_C' -A 1 "ancestral_sequences_3.fasta"
>sample_C
AANAA

Expand All @@ -104,17 +104,17 @@ Note 2: TreeTime chooses the root state as G as well, so there's no mutation on
$ ${AUGUR} ancestral --seed 0 \
> --infer-ambiguous \
> --tree $TESTDIR/../data/simple-genome/tree.nwk --alignment aln_pos3X.fasta \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations_4.json" \
> --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences_4.fasta" &> /dev/null
> --output-node-data "ancestral_mutations_4.json" \
> --output-sequences "ancestral_sequences_4.fasta" &> /dev/null


$ cat "$CRAMTMP/$TESTFILE/ancestral_mutations_4.json" | jq -c '.nodes.sample_C.muts'
$ cat "ancestral_mutations_4.json" | jq -c '.nodes.sample_C.muts'
[]

$ cat "$CRAMTMP/$TESTFILE/ancestral_mutations_4.json" | jq -c '.nodes.sample_C.sequence'
$ cat "ancestral_mutations_4.json" | jq -c '.nodes.sample_C.sequence'
"AAGAA"

$ grep 'sample_C' -A 1 "$CRAMTMP/$TESTFILE/ancestral_sequences_4.fasta"
$ grep 'sample_C' -A 1 "ancestral_sequences_4.fasta"
>sample_C
AAGAA

Expand All @@ -135,11 +135,11 @@ should report 'N' (the standard ambiguous nucleotide) when we're not inferring a
$ ${AUGUR} ancestral --seed 0 \
> --keep-ambiguous \
> --tree $TESTDIR/../data/simple-genome/tree.nwk --alignment aln_pos3X_internal.fasta \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations_5.json" \
> --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences_5.fasta" &> /dev/null
> --output-node-data "ancestral_mutations_5.json" \
> --output-sequences "ancestral_sequences_5.fasta" &> /dev/null


$ cat "$CRAMTMP/$TESTFILE/ancestral_mutations_5.json" | jq -c '.nodes.node_AB.sequence'
$ cat "ancestral_mutations_5.json" | jq -c '.nodes.node_AB.sequence'
"AANAA"


Expand All @@ -166,15 +166,15 @@ The reference 'X' at pos 3 should be equivalent to 'N')
> --keep-ambiguous \
> --root-sequence ref_pos3X.fasta \
> --tree $TESTDIR/../data/simple-genome/tree.nwk --alignment aln_col3N.fasta \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations_6.json" \
> --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences_6.fasta" &> /dev/null
> --output-node-data "ancestral_mutations_6.json" \
> --output-sequences "ancestral_sequences_6.fasta" &> /dev/null


$ cat "$CRAMTMP/$TESTFILE/ancestral_mutations_6.json" | jq -c '[.nodes[].sequence] | unique'
$ cat "ancestral_mutations_6.json" | jq -c '[.nodes[].sequence] | unique'
["AANAA"]

$ cat "$CRAMTMP/$TESTFILE/ancestral_mutations_6.json" | jq -c '[.nodes[].muts[]]'
$ cat "ancestral_mutations_6.json" | jq -c '[.nodes[].muts[]]'
[]

$ cat "$CRAMTMP/$TESTFILE/ancestral_mutations_6.json" | jq -c '.reference.nuc'
$ cat "ancestral_mutations_6.json" | jq -c '.reference.nuc'
"AANAA"
16 changes: 8 additions & 8 deletions tests/functional/ancestral/cram/infer-amino-acid-sequences-multiple-genes-no-nuc.t
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Expand Up @@ -12,28 +12,28 @@ Infer multiple genes with a provided GenBank annotation file
> --genes ENV PRO \
> --translations $TESTDIR/../data/aa_sequences_%GENE.fasta \
> --seed 314159 \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations_1.json" \
> --output-translations "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_%GENE_1.fasta" &> /dev/null
> --output-node-data "ancestral_mutations_1.json" \
> --output-translations "ancestral_aa_sequences_%GENE_1.fasta" &> /dev/null

Check that the annotations block only includes ENV & PRO, not nuc

$ grep -E "\"(ENV|PRO|nuc)\": {" "$CRAMTMP/$TESTFILE/ancestral_mutations_1.json"
$ grep -E "\"(ENV|PRO|nuc)\": {" "ancestral_mutations_1.json"
"ENV": {
"PRO": {

Check that amino acid sequences exist for the root node of the tree.

$ grep -A 2 "aa_sequences" "$CRAMTMP/$TESTFILE/ancestral_mutations_1.json"
$ grep -A 2 "aa_sequences" "ancestral_mutations_1.json"
"aa_sequences": {
"ENV": .* (re)
"PRO": .* (re)

Check that internal nodes have ancestral amino acid sequences.

$ grep "NODE" "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_ENV_1.fasta" | wc -l
$ grep "NODE" "ancestral_aa_sequences_ENV_1.fasta" | wc -l
\s*8 (re)

$ grep "NODE" "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_PRO_1.fasta" | wc -l
$ grep "NODE" "ancestral_aa_sequences_PRO_1.fasta" | wc -l
\s*8 (re)


Expand All @@ -46,7 +46,7 @@ Catches this bug <https://github.com/nextstrain/augur/pull/1958#discussion_r3034
> --genes $TESTDIR/../data/genes.txt \
> --translations $TESTDIR/../data/aa_sequences_ENV.fasta \
> --seed 314159 \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations_error.json" \
> --output-translations "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_error.fasta" > /dev/null
> --output-node-data "ancestral_mutations_error.json" \
> --output-translations "ancestral_aa_sequences_error.fasta" > /dev/null
ERROR: --translations must contain %GENE for multiple-gene amino acid reconstructions
[2]
40 changes: 20 additions & 20 deletions tests/functional/ancestral/cram/infer-amino-acid-sequences-single-gene-no-nuc.t
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Expand Up @@ -12,24 +12,24 @@ Firstly a single gene (ENV), using a hardcoded fasta path, and an annotation fil
> --genes ENV \
> --translations $TESTDIR/../data/aa_sequences_ENV.fasta \
> --seed 314159 \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations_1.json" \
> --output-translations "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_ENV_1.fasta" &> /dev/null
> --output-node-data "ancestral_mutations_1.json" \
> --output-translations "ancestral_aa_sequences_ENV_1.fasta" &> /dev/null

Check that the annotations block only includes ENV, not nuc or PRO

$ grep -E "\"(ENV|PRO|nuc)\": {" "$CRAMTMP/$TESTFILE/ancestral_mutations_1.json"
$ grep -E "\"(ENV|PRO|nuc)\": {" "ancestral_mutations_1.json"
"ENV": {

Check that amino acid sequences exist for the root node of the tree.

$ grep -A 2 "aa_sequences" "$CRAMTMP/$TESTFILE/ancestral_mutations_1.json"
$ grep -A 2 "aa_sequences" "ancestral_mutations_1.json"
"aa_sequences": {
"ENV": .* (re)
}

Check that internal nodes have ancestral amino acid sequences.

$ grep "NODE" "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_ENV_1.fasta" | wc -l
$ grep "NODE" "ancestral_aa_sequences_ENV_1.fasta" | wc -l
\s*8 (re)


Expand All @@ -41,14 +41,14 @@ And the exact same, but using a %GENE pattern in the filepath
> --genes ENV \
> --translations $TESTDIR/../data/aa_sequences_%GENE.fasta \
> --seed 314159 \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations_2.json" \
> --output-translations "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_%GENE_2.fasta" &> /dev/null
> --output-node-data "ancestral_mutations_2.json" \
> --output-translations "ancestral_aa_sequences_%GENE_2.fasta" &> /dev/null

Check that the outputs are identical

$ diff "$CRAMTMP/$TESTFILE/ancestral_mutations_1.json" "$CRAMTMP/$TESTFILE/ancestral_mutations_2.json"
$ diff "ancestral_mutations_1.json" "ancestral_mutations_2.json"

$ diff "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_ENV_1.fasta" "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_ENV_2.fasta"
$ diff "ancestral_aa_sequences_ENV_1.fasta" "ancestral_aa_sequences_ENV_2.fasta"


For single genes the annotations file is optional. The result should be the same except the (nuc) coordinates of the CDS will differ without the annotation file
Expand All @@ -58,16 +58,16 @@ For single genes the annotations file is optional. The result should be the same
> --genes ENV \
> --translations $TESTDIR/../data/aa_sequences_ENV.fasta \
> --seed 314159 \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations_3.json" \
> --output-translations "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_ENV_3.fasta" &> /dev/null
> --output-node-data "ancestral_mutations_3.json" \
> --output-translations "ancestral_aa_sequences_ENV_3.fasta" &> /dev/null


$ diff "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_ENV_1.fasta" "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_ENV_3.fasta"
$ diff "ancestral_aa_sequences_ENV_1.fasta" "ancestral_aa_sequences_ENV_3.fasta"

Nucleotide coordinates of the ENV gene are different - without the annotation file we start them at nuc_pos=1 (1-based, GFF-style)
So for this example the offset is 960 (start is 961 - 960 = 1, end is 2472 - 960 = 1512)
So for this example the offset is 960 (start is 961 - 960 = 1, end is 2472 - 960 = 1512)

$ diff "$CRAMTMP/$TESTFILE/ancestral_mutations_1.json" "$CRAMTMP/$TESTFILE/ancestral_mutations_3.json"
$ diff "ancestral_mutations_1.json" "ancestral_mutations_3.json"
4,6c4,5
\< "end": 2472, (re)
\< "seqid": .* (re)
Expand All @@ -88,18 +88,18 @@ Test single gene reconstruction with an explicitly provided AA root-sequence
> --translations $TESTDIR/../data/aa_sequences_ENV.fasta \
> --aa-root-sequence $TESTDIR/../data/ENV_outgroup.fasta \
> --seed 314159 \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations_4.json" &> /dev/null
> --output-node-data "ancestral_mutations_4.json" &> /dev/null

The reference has been modified to include a leading AAA:

$ grep -A 2 "reference" "$CRAMTMP/$TESTFILE/ancestral_mutations_4.json"
$ grep -A 2 "reference" "ancestral_mutations_4.json"
"reference": {
"ENV": "AAA.+ (re)
}

Check that this results in 3 mutations between the provided root-sequence & the inferred root node

$ grep -A 11 "NODE_0000006" "$CRAMTMP/$TESTFILE/ancestral_mutations_4.json"
$ grep -A 11 "NODE_0000006" "ancestral_mutations_4.json"
"NODE_0000006": {
"aa_muts": {
"ENV": [
Expand All @@ -123,10 +123,10 @@ Retest the above, using a %GENE placeholder in --aa-root-sequence
> --translations $TESTDIR/../data/aa_sequences_ENV.fasta \
> --aa-root-sequence $TESTDIR/../data/%GENE_outgroup.fasta \
> --seed 314159 \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations_5.json" &> /dev/null
> --output-node-data "ancestral_mutations_5.json" &> /dev/null


$ diff "$CRAMTMP/$TESTFILE/ancestral_mutations_4.json" "$CRAMTMP/$TESTFILE/ancestral_mutations_5.json"
$ diff "ancestral_mutations_4.json" "ancestral_mutations_5.json"


Test that accidentally providing the wrong AA root-sequence (e.g. a nuc one) results in an error
Expand All @@ -138,6 +138,6 @@ Test that accidentally providing the wrong AA root-sequence (e.g. a nuc one) res
> --translations $TESTDIR/../data/aa_sequences_ENV.fasta \
> --aa-root-sequence $TESTDIR/../data/simple-genome/reference.fasta \
> --seed 314159 \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations_5.json" > /dev/null
> --output-node-data "ancestral_mutations_5.json" > /dev/null
ERROR: The provided root-sequence AA fasta for ENV has length 50 which doesn't match the length of the CDS 504 (amino acids)
[2]
4 changes: 2 additions & 2 deletions tests/functional/ancestral/cram/infer-amino-acid-sequences-with-root-sequence.t
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Expand Up @@ -16,12 +16,12 @@ ancestor).
> --genes ENV PRO \
> --translations $TESTDIR/../data/aa_sequences_%GENE.fasta \
> --seed 314159 \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" &> /dev/null
> --output-node-data "ancestral_mutations.json" &> /dev/null

Check that the reference length was correctly exported as the nuc annotation

$ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
> --exclude-regex-paths "['seqid']" -- \
> "$TESTDIR/../data/ancestral_mutations_with_root_sequence.json" \
> "$CRAMTMP/$TESTFILE/ancestral_mutations.json"
> "ancestral_mutations.json"
{}
12 changes: 6 additions & 6 deletions tests/functional/ancestral/cram/infer-amino-acid-sequences.t
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Expand Up @@ -11,25 +11,25 @@ Infer ancestral nucleotide and amino acid sequences.
> --genes ENV PRO \
> --translations $TESTDIR/../data/aa_sequences_%GENE.fasta \
> --seed 314159 \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" \
> --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" \
> --output-translations "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_%GENE.fasta" &> /dev/null
> --output-node-data "ancestral_mutations.json" \
> --output-sequences "ancestral_sequences.fasta" \
> --output-translations "ancestral_aa_sequences_%GENE.fasta" &> /dev/null

Check that the reference length was correctly exported as the nuc annotation

$ grep -E "\"(ENV|PRO|nuc)\": {" "$CRAMTMP/$TESTFILE/ancestral_mutations.json"
$ grep -E "\"(ENV|PRO|nuc)\": {" "ancestral_mutations.json"
"ENV": {
"PRO": {
"nuc": {

Check that amino acid sequences exist for the root node of the tree.

$ grep -A 2 "aa_sequences" "$CRAMTMP/$TESTFILE/ancestral_mutations.json"
$ grep -A 2 "aa_sequences" "ancestral_mutations.json"
"aa_sequences": {
"ENV": .* (re)
"PRO": .* (re)

Check that internal nodes have ancestral amino acid sequences.

$ grep "NODE" "$CRAMTMP/$TESTFILE/ancestral_aa_sequences_ENV.fasta" | wc -l
$ grep "NODE" "ancestral_aa_sequences_ENV.fasta" | wc -l
\s*8 (re)
6 changes: 3 additions & 3 deletions tests/functional/ancestral/cram/keep-ambiguous-nucleotides.t
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Expand Up @@ -10,8 +10,8 @@ There should be N bases in the inferred output sequences.
> --alignment $TESTDIR/../data/aligned.fasta \
> --keep-ambiguous \
> --seed 314159 \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" \
> --output-sequences "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" &> /dev/null
> --output-node-data "ancestral_mutations.json" \
> --output-sequences "ancestral_sequences.fasta" &> /dev/null

$ grep "^N" "$CRAMTMP/$TESTFILE/ancestral_sequences.fasta" | head -n 1
$ grep "^N" "ancestral_sequences.fasta" | head -n 1
NNNNNNNNNNNNGACAGTTCGAGTTTGAAGCGAAAGCTAGCAACAGTATCAACAGGTTTT
5 changes: 1 addition & 4 deletions tests/functional/curate/cram/titlecase.t
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@@ -1,8 +1,6 @@
Setup

$ pushd "$TESTDIR" > /dev/null
$ export AUGUR="${AUGUR:-../../../../bin/augur}"

$ source "$TESTDIR"/_setup.sh

Test output with articles and a mixture of lower and uppercase letters.

Expand Down Expand Up @@ -96,4 +94,3 @@ Test silencing on failures such as when encountering a non-string value
> | ${AUGUR} curate titlecase --titlecase-fields "bare_int" \
> --failure-reporting "silent"
{"bare_int": 2021}

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