seismic table

Purpose

seismic table summarizes per-position and per-read mutation data into CSV files that can be opened in spreadsheet software or used for plotting. Run it after Filter, Cluster, or Join to get the mutation rates and read counts that power downstream graphs and structure prediction.

Inputs

IDmut, Filter, Cluster, or Join output directories or report files: One or more paths. See Specify Input Files.

Outputs

Output files go into the same directory as the input report they summarize.

Per-position tables

{step}-position-table.csv: One row per reference position; columns include mutation rate, informative read count, and per-type mutation counts.

Per-read tables

{step}-read-table.csv: One row per read; columns include the number of mutations.

Per-cluster tables

cluster-abundance-table.csv: For Cluster data, one row per cluster with its number of reads.

Quick example

Tabulate filter output for sample-1:

seismic table out/sample-1/filter/ref-1

Tabulate everything in the output directory:

seismic table out/

Options

Toggle which tables to write

--idmut-pos-table/--no-idmut-pos-table: Write per-position table for IDmut data (default on).
--idmut-read-table/--no-idmut-read-table: Write per-read table for IDmut data (default off).
--filter-pos-table/--no-filter-pos-table: Write per-position table for Filter data (default on).
--filter-read-table/--no-filter-read-table: Write per-read table for Filter data (default on).
--cluster-pos-table/--no-cluster-pos-table: Write per-position table for Cluster data (default on).
--cluster-abundance-table/--no-cluster-abundance-table: Write per-cluster read-count table for Cluster data (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.