Using the --pipe argument

The --pipe flag lets traceratops commands read lists of trace files from standard input. This is handy when you want to reuse shell tools such as find, ls, or cat to build flexible file lists without typing them all on the command line. Commands accept one filename per line.

Filter traces discovered with find

Use find to collect all trace tables in a directory tree, then pipe the list into trace_filter for batch processing:

find /data/experiment_42 -name "*.ecsv" \
  | trace_filter --pipe --n_barcodes 3

This scans every .ecsv file under /data/experiment_42 and filters them in a single run.

Plot interactions from a saved list

If you already have a text file listing the traces you want to analyze, feed it to plotting commands with cat and --pipe:

cat trace_files.txt | plot_4m --pipe --anchor 18 --cutoff 0.20

Here trace_files.txt contains one trace path per line. The command produces a 4M interaction plot for anchor barcode 18 with a 0.20 cutoff.

Analyze traces with other tools

Most traceratops CLI tools that accept trace files support --pipe, so you can mix and match pipelines. For example, to run quality analysis across all traces in the current directory:

ls *.ecsv | trace_analyzer --pipe

This reads every listed trace and computes the analysis in one pass.