seismic export
Purpose
seismic export converts SEISMIC-RNA table data into JSON files formatted
for import into external tools.
It is off by default in seismic wf; enable it with --export.
Inputs
- Table CSV files or output directories
Per-position mutation rate tables from
seismic table. See Specify Input Files.
Outputs
{sample}__webapp.jsonAll of the sample’s data in one JSON file, written to the top of the output directory (one file per sample).
Quick example
Export all table output for sample-1:
seismic export out/sample-1/filter/ref-1
Options
- Metadata
--samples-meta FILE(-S)CSV file of sample metadata to embed in exported results. See Metadata for Samples.
--refs-meta FILE(-R)CSV file of reference metadata to embed in exported results. See Metadata for References.
- Positions
--all-pos/--unmasked-posExport all positions (on) or only unmasked positions (off). Default: on.
- Performance
--num-cpus N— multiprocessing; see Parallelize Tasks.--force— overwrite existing outputs.
The auto-generated Command Line Reference lists every option with its current default.
See also
seismic table — produces the CSV tables this step exports