augur sequence-traitsļƒ

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 Argumentsļƒ

--ancestral-sequences

nucleotide alignment (VCF) to search for sequence traits in (can be generated from ā€˜ancestralā€™ using ā€˜ā€“output-vcfā€™)

--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: ā€œGENE SITE ALT DISPLAY_NAME FEATUREā€. For nucleotide sites, GENE can be ā€œnucā€ (or column excluded entirely for all-nuc sites). ā€œDISPLAY_NAMEā€ can be blank or excluded entirely.

--count

Possible choices: traits, mutations

Whether to count traits (ex: # drugs resistant to) or mutations

Default: ā€œtraitsā€

--label

How to label the counts (ex: Drug_Resistance)

Default: ā€œ# Traitsā€

--output-node-data

name of JSON file to save sequence features to