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Configuration Examples

This directory contains example configuration files for Pattern Analyzer in both JSON and YAML formats. These files demonstrate how to customize an analysis pipeline.

Files

  • example.json: An example configuration using JSON syntax.
  • example.yml: An equivalent example using YAML syntax.

Configuration Structure

You can use a configuration file with the CLI (-c or --config flag) or pass a dictionary with the same structure to the engine.analyze() method in the Python API.

The main top-level keys are:

  • transforms: A list of data transformation plugins to apply sequentially before analysis. Each item can be a simple string (the plugin name) or a dictionary specifying a name and params.
  • tests: A list of test plugins to run on the (potentially transformed) data. The structure is the same as for transforms.
  • fdr_q: (Optional) A float between 0 and 1 specifying the significance level (q-value) for the False Discovery Rate (FDR) correction. This helps control for false positives when running multiple tests. Defaults to 0.05.
  • html_report: (Optional) A file path where a standalone HTML report will be generated.
  • log_path: (Optional) A file path where detailed, structured (JSONL) logs will be written during the analysis.

Example Usage (CLI)

You can run an analysis using one of the example configuration files like this:

# Using the YAML configuration
patternanalyzer analyze my_data.bin --config docs/configs/example.yml

# Using the JSON configuration
patternanalyzer analyze my_data.bin --config docs/configs/example.json