augur sequence-traits¶
Annotate sequences based on amino-acid or nucleotide signatures.
usage: augur sequence-traits [-h] [--ancestral-sequences ANCESTRAL_SEQUENCES]
[--translations TRANSLATIONS]
[--vcf-reference VCF_REFERENCE]
[--vcf-translate-reference VCF_TRANSLATE_REFERENCE]
[--features FEATURES]
[--count {traits,mutations}] [--label LABEL]
[--output-node-data OUTPUT_NODE_DATA]
Named Arguments¶
- --ancestral-sequences
nucleotide alignment (VCF) to search for sequence traits in (can be generated from ‘ancestral’ using ‘–output-vcf’)
- --translations
AA alignment to search for sequence traits in (can include ancestral sequences)
- --vcf-reference
fasta file of the sequence the nucleotide VCF was mapped to
- --vcf-translate-reference
fasta file of the sequence the translated VCF was mapped to
- --features
file that specifies sites defining the features in a tab-delimited format: “GENE SITE ALT DISPLAY_NAME FEATURE”. For nucleotide sites, GENE can be “nuc” (or column excluded entirely for all-nuc sites). “DISPLAY_NAME” can be blank or excluded entirely.
- --count
Possible choices: traits, mutations
Whether to count traits (ex: # drugs resistant to) or mutations
Default: “traits”
- --label
How to label the counts (ex: Drug_Resistance)
Default: “# Traits”
- --output-node-data
name of JSON file to save sequence features to