apply-record-annotations

Applies record annotations to overwrite field values. This does not do any additional transformations on top of the annotations.

usage: augur curate apply-record-annotations [-h] [--metadata METADATA]
                                             [--id-column ID_COLUMN]
                                             [--metadata-delimiters METADATA_DELIMITERS [METADATA_DELIMITERS ...]]
                                             [--fasta FASTA]
                                             [--seq-id-column SEQ_ID_COLUMN]
                                             [--seq-field SEQ_FIELD]
                                             [--unmatched-reporting {error_first,error_all,warn,silent}]
                                             [--duplicate-reporting {error_first,error_all,warn,silent}]
                                             [--output-metadata OUTPUT_METADATA]
                                             [--output-fasta OUTPUT_FASTA]
                                             [--output-id-field OUTPUT_ID_FIELD]
                                             [--output-seq-field OUTPUT_SEQ_FIELD]
                                             --annotations TSV
                                             [--id-field ID_FIELD]

Named Arguments

--annotations

Manually curated annotations TSV file. The TSV should not have a header and should have exactly three columns: id to match existing metadata, field name, and field value. If there are multiple annotations for the same id and field, then the last value is used. Lines starting with β€˜#’ are treated as comments. Any β€˜#’ after the field value are treated as comments.

--id-field

The ID field in the metadata to use to merge with the annotations.

Default: 'accession'

INPUTS

Input options shared by all augur curate commands. If no input options are provided, commands will try to read NDJSON records from stdin.

--metadata

Input metadata file. May be plain text (TSV, CSV) or an Excel or OpenOffice spreadsheet workbook file. When an Excel or OpenOffice workbook, only the first visible worksheet will be read and initial empty rows/columns will be ignored. Accepts β€˜-’ to read plain text from stdin.

--id-column

Name of the metadata column that contains the record identifier for reporting duplicate records. Uses the first column of the metadata file if not provided. Ignored if also providing a FASTA file input.

--metadata-delimiters

Delimiters to accept when reading a plain text metadata file. Only one delimiter will be inferred.

Default: (',', '\t')

--fasta

Plain or gzipped FASTA file. Headers can only contain the sequence id used to match a metadata record. Note that an index file will be generated for the FASTA file as <filename>.fasta.fxi

--seq-id-column

Name of metadata column that contains the sequence id to match sequences in the FASTA file.

--seq-field

The name to use for the sequence field when joining sequences from a FASTA file.

--unmatched-reporting

Possible choices: error_first, error_all, warn, silent

How unmatched records from combined metadata/FASTA input should be reported.

Default: error_first

--duplicate-reporting

Possible choices: error_first, error_all, warn, silent

How should duplicate records be reported.

Default: error_first

OUTPUTS

Output options shared by all augur curate commands. If no output options are provided, commands will output NDJSON records to stdout.

--output-metadata

Output metadata TSV file. Accepts β€˜-’ to output TSV to stdout.

--output-fasta

Output FASTA file.

--output-id-field

The record field to use as the sequence identifier in the FASTA output.

--output-seq-field

The record field that contains the sequence for the FASTA output. This field will be deleted from the metadata output.