augur translate

Command-line arguments

Translate gene regions from nucleotides to amino acids.

Translates nucleotide sequences of nodes in a tree to amino acids for gene regions of the annotated features of the provided reference sequence. Each node then gets assigned a list of amino acid mutations for any position that has a mismatch between its own amino acid sequence and its parent’s sequence. The reference amino acid sequences, genome annotations, and node amino acid mutations are output to a node-data JSON file.

Note

The mutation positions in the node-data JSON are one-based.

usage: augur translate [-h] [--config CONFIG] --tree TREE
                       --ancestral-sequences ANCESTRAL_SEQUENCES
                       --reference-sequence REFERENCE_SEQUENCE
                       [--genes GENES [GENES ...]]
                       [--output-node-data OUTPUT_NODE_DATA]
                       [--alignment-output ALIGNMENT_OUTPUT]
                       [--validation-mode {error,warn,skip}]
                       [--skip-validation] [--vcf-reference VCF_REFERENCE]
                       [--vcf-reference-output VCF_REFERENCE_OUTPUT]

Named Arguments

--config

config file path

--tree

prebuilt Newick -- no tree will be built if provided

--ancestral-sequences

JSON (fasta input) or VCF (VCF input) containing ancestral and tip sequences

--reference-sequence

GenBank or GFF file containing the annotation

--genes

genes to translate (list or file containing list)

--output-node-data

name of JSON file to save aa-mutations to

--alignment-output

write out translated gene alignments. If a VCF-input, a .vcf or .vcf.gz will be output here (depending on file ending). If fasta-input, specify the file name like so: ‘my_alignment_%GENE.fasta’, where ‘%GENE’ will be replaced by the name of the gene

--validation-mode

Possible choices: error, warn, skip

Control if optional validation checks are performed and what happens if they fail.

‘error’ and ‘warn’ modes perform validation and emit messages about failed validation checks. ‘error’ mode causes a non-zero exit status if any validation checks failed, while ‘warn’ does not.

‘skip’ mode performs no validation.

Note that some validation checks are non-optional and as such are not affected by this setting.

Default: error

--skip-validation

Skip validation of input/output files, equivalent to a ‘--validation-mode’/’validation_mode’ value of ‘skip’. Use at your own risk!

VCF specific

These arguments are only applicable if the input (‘--ancestral-sequences’/’ancestral_sequences’) is in VCF format.

--vcf-reference

fasta file of the sequence the VCF was mapped to

--vcf-reference-output

fasta file where reference sequence translations for VCF input will be written

Configuration

Options can also be specified in a YAML configuration file supplied to --config with the following top-level keys:

Option	Type	Description
tree	file	prebuilt Newick -- no tree will be built if provided
ancestral_sequences	file	JSON (fasta input) or VCF (VCF input) containing ancestral and tip sequences
reference_sequence	file	GenBank or GFF file containing the annotation
genes	string(s)	genes to translate (list or file containing list)
output_node_data	string	name of JSON file to save aa-mutations to
alignment_output	string	write out translated gene alignments. If a VCF-input, a .vcf or .vcf.gz will be output here (depending on file ending). If fasta-input, specify the file name like so: ‘my_alignment_%%GENE.fasta’, where ‘%%GENE’ will be replaced by the name of the gene
validation_mode	one of: error warn skip	Control if optional validation checks are performed and what happens if they fail. ‘error’ and ‘warn’ modes perform validation and emit messages about failed validation checks. ‘error’ mode causes a non-zero exit status if any validation checks failed, while ‘warn’ does not. ‘skip’ mode performs no validation. Note that some validation checks are non-optional and as such are not affected by this setting.
skip_validation	string	Skip validation of input/output files, equivalent to a ‘--validation-mode’/’validation_mode’ value of ‘skip’. Use at your own risk!
vcf_reference	file	fasta file of the sequence the VCF was mapped to
vcf_reference_output	string	fasta file where reference sequence translations for VCF input will be written

Example Node Data JSON

Here’s an example of the output node-data JSON where NODE_1 has no mutations compared to it’s parent and NODE_2 has multiple mutations in multiple genes.

{
    "annotations": {
        "GENE_1": {
            "end": 1685,
            "seqid": "reference.gb",
            "start": 108,
            "strand": "+",
            "type": "CDS"
        },
        "GENE_2": {
            "end": 2705,
            "seqid": "reference.gb",
            "start": 1807,
            "strand": "+",
            "type": "CDS"
        },
    },
    "nodes": {
        "NODE_1": {
            "aa_muts": []
        },
        "NODE_2": {
            "aa_muts": [
                "GENE_1": [
                    "S139N",
                    "R213K",
                    "R439G",
                    "V440A",
                    "D474N",
                    "S479W",
                    "S481T",
                    "P485L",
                    "R521K"
                ],
                "GENE_2": [
                    "P43S",
                    "D46N",
                    "C64R",
                    "R98K",
                    "D136G",
                    "M175V"
                ]
            ]
        }
    },
    "reference": {
        "GENE_1": "MATLLRSLAL...",
        "GENE_2": "MAEEQARHVK..."
    }
}