trace_stats

Reliability status: stable

This script reads a chromatin trace file and computes basic statistics:

Number of unique ROIs
Number of unique chromatin traces

usage: trace_stats [-h] (--input INPUT | --pipe)

Named Arguments

--input

Path to the input trace file.

--pipe

Read trace filenames from stdin (pipe).

Default: False

Output Files

The script does not write output files. It reports trace statistics in the terminal:

terminal output: Summary containing the number of unique ROIs, chromatin traces, and barcodes in the input trace table.

Statistics for merged_traces.ecsv:
- Number of unique ROIs: 3
- Number of unique chromatin traces: 6115
- Number of unique barcodes: 86

Examples

trace_stats.py --input traces_KC_AB_merged.ecsv

Terminal output:

$ Importing table from pyHiM format
Successfully loaded trace table: traces_KC_AB_merged.ecsv
Statistics for traces_KC_AB_merged.ecsv:
- Number of unique ROIs: 26
- Number of unique chromatin traces: 7573

Notes

See the command-line reference above for the complete option list.