locate

atb agc locate

Look up which AGC batch (and OSF part) holds each accession

Synopsis

Resolve sample accessions to the AGC batch that contains them, without downloading anything. This is the search half of 'atb agc download': it answers "which batch is my sample in, and is that batch available yet?".

Accessions come from positional arguments, a --from file (a query result with a sample_accession column, or one accession per line; - for stdin), or piped stdin. The accession->batch map and the batch index are fetched and cached exactly as 'atb agc download' fetches them; no agc binary is required.

atb agc locate [accession...] [flags]

Examples

  # One accession
  atb agc locate SAMEA2247573

  # A whole query result, as JSON for a pipeline
  atb query --species "Escherichia coli" --limit 5 --format tsv | \
    atb agc locate --from - --format json

Options

      --format string   output format: tsv or json (default "tsv")
      --from string     CSV/TSV with a sample_accession column, or one accession per line (- for stdin)
  -h, --help            help for locate
      --refresh         re-fetch the accession->batch map and the batch index even if cached

Options inherited from parent commands

      --config string     config file (default $HOME/.atb/config.toml)
      --data-dir string   directory for the local metadata index (default ~/.local/share/atb/data; override with $ATB_DATA_DIR)

SEE ALSO

• atb agc - Download and inspect genomes in AGC archives