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Improved ancestral translation validation #1321

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Improved ancestral translation validation #1321

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15 changes: 13 additions & 2 deletions augur/ancestral.py
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Original file line number Diff line number Diff line change
Expand Up @@ -231,8 +231,19 @@ def register_parser(parent_subparsers):
def run(args):
# Validate arguments.
aa_arguments = (args.annotation, args.genes, args.translations)
if any(aa_arguments) and not all(aa_arguments):
raise AugurError("For amino acid sequence reconstruction, you must provide an annotation file, a list of genes, and a template path to amino acid sequences.")
if any(aa_arguments):
if not all(aa_arguments):
# Find missing arguments.
missing = []
if not args.annotation:
missing.append("annotation file (--annotation)")
if not args.genes:
missing.append("gene list (--genes)")
if not args.translations:
missing.append("template path to amino acid sequences (--translations)")
raise AugurError("For amino acid sequence reconstruction, you must also provide the following arguments: " + ", ".join(missing))
if "%GENE" not in args.translations:
raise AugurError(f"The template string for translations must contain the substring %GENE. You provided: {args.translations}")

# check alignment type, set flags, read in if VCF
is_vcf = any([args.alignment.lower().endswith(x) for x in ['.vcf', '.vcf.gz']])
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2 changes: 1 addition & 1 deletion tests/functional/ancestral/cram/infer-amino-acid-sequences-with-missing-arguments.t
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Expand Up @@ -11,5 +11,5 @@ This should fail.
> --annotation $TESTDIR/../data/zika_outgroup.gb \
> --genes ENV PRO \
> --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" > /dev/null
ERROR: For amino acid sequence reconstruction, you must provide an annotation file, a list of genes, and a template path to amino acid sequences.
ERROR: For amino acid sequence reconstruction, you must also provide the following arguments: template path to amino acid sequences (--translations)
[2]
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