AdvancedAnalysisFileParser 0.1.3

Parse Illumina-DRAGEN TSV/JSON outputs to unified geneyx JSON with warnings.

AdvancedAnalysisFileParser

A Python package to parse Illumina-DRAGEN "special caller" outputs (TSV/JSON) into a unified JSON format, with automatic warnings based on user-defined or default conditions. Supports oncology, GBA, SMN, HBA, and more.

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Features

• Unified JSON output for multiple DRAGEN caller types (TSV/JSON)
• Automatic warnings for each file type, based on config or defaults
• Pluggable parser architecture for new file types
• CLI and Python API usage
• Example configs and test data included

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Installation

Install from PyPI (recommended):

pip install AdvancedAnalysisFileParser

Or from source:

git clone https://github.com/geneyx/geneyx.analysis.api.git
cd geneyx.analysis.api/scripts/AdvancedAnalysisFileParser
pip install -e .

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Quickstart

Python API Usage

from AdvancedAnalysisFileParser.AdvancedAnalysisParser import AdvancedAnalysisParser

request = {
		"input_dir": "./Test",
		"output_dir": "./Test",
		"output_json": "adv_output.json",
		# Optionally, you can specify input_files or map_files for custom configs
}
parser = AdvancedAnalysisParser(request)
parser.run()  # writes output to adv_output.json

# Or get result as dict:
result = parser.run(return_dict=True)
print(result)

Command-Line Usage

Create a config file (e.g. config.json):

{
	"input_dir": "./Test",
	"output_dir": "./Test",
	"output_json": "adv_output.json"
}

Then run:

python -m AdvancedAnalysisFileParser.AdvancedAnalysisParser -c config.json

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Configuration

The parser uses config files (JSON) to define how to parse and warn for each file type. Default configs are provided for:

• GBA: gba_tsv_config.json
• SMN: smn_tsv_config.json
• Oncology: dragen_500_tsv_config.json
• JSON: dragen_targeted_config.json

You can override or extend these by providing your own config in the map_files key of the request.

Example request/config structure

Key	Type	Description
output_json	string	Filename for the generated JSON (default: adv_analysis_output.json)
input_dir	string	Directory containing all input files
input_files	list	(Optional) List of files to parse
map_files	object	(Optional) Mapping of filenames → caller definitions

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Warnings

Warnings are generated automatically for each caller/file type, based on the config. Each config defines conditions for warnings (see *_config.json files for examples). You can customize these for your use case.

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Testing

Run the test suite to validate all parsing and warning logic:

pytest AdvancedAnalysisFileParser/Test_AdvancedAnalysisParser.py

Or run the test script:

python AdvancedAnalysisFileParser/run_test_parser.py

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Example Data

See the Test/ folder for example input files (TSV/JSON) and expected outputs.

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License

MIT