seismic join

Purpose

seismic join concatenates two or more regions of a reference into a single joined region. Use it when you defined separate regions (e.g. two amplicons on the same RNA) and want to analyze or visualize them as one continuous stretch. The original regions are not modified; join creates a new virtual region.

Inputs

Filter, Cluster, or Join output directories or report files: One or more paths to the regions you want to join. All inputs must belong to the same sample and reference. See Specify Input Files.
Joined region name: First positional argument: the name to give the new joined region.

Outputs

All outputs go into {out}/{sample}/{step}/{ref}/{joined-region}/, where {step} is filter or cluster depending on the inputs.

filter-report.json or cluster-report.json: Join report describing which regions were combined. See Join Report. Named to match its source so downstream steps (Table) accept it interchangeably with Filter/Cluster reports.

Quick example

Join two amplicon regions into one:

seismic join joined out/sample-1/filter/ref-1/amp-1 out/sample-1/filter/ref-1/amp-2

To join all regions in the output directory:

seismic join joined out/

Options

Cluster assignment

--join-clusts FILE (-j): CSV file specifying which cluster of each input region maps to which cluster of the joined region (optional). See Metadata for Joined Clusters.

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.

Common unexpected results

Warning: duplicate regions: An original region appears more than once among the inputs. This is harmless — it will not be double-counted — but check that the resulting joined region contains exactly what you intended.
Error: would overwrite existing non-joined region: You chose a name that already exists as a real region. Choose a different name or remove the conflicting directory first.