Metadata-Version: 2.2
Name: dragen-results-utils
Version: 0.1.0
Summary: Collection of Python scripts for post-processing Illumina DRAGEN results output files.
Author-email: Jaideep Sundaram <jai.python3@gmail.com>
Maintainer-email: Jaideep Sundaram <jai.python3@gmail.com>
License: Not open source
Project-URL: Homepage, https://github.com/jai-python3/dragen-results-utils
Keywords: Illumina,DRAGEN,post-processing
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.10
Requires-Python: >=3.10
Description-Content-Type: text/x-rst
License-File: AUTHORS.rst
Requires-Dist: Click>=7.0
Requires-Dist: PyYAML
Requires-Dist: Rich
Requires-Dist: singleton-decorator
Requires-Dist: pandas
Requires-Dist: matplotlib
Requires-Dist: seaborn
Provides-Extra: dev
Requires-Dist: coverage; extra == "dev"
Requires-Dist: mypy; extra == "dev"
Requires-Dist: pytest; extra == "dev"
Requires-Dist: ruff; extra == "dev"

====================
DRAGEN Results Utils
====================

Collection of Python scripts for post-processing Illumina DRAGEN results output files.

Exported Console scripts
------------------------

* analyze-dragen-results

.. code-block:: bash

    analyze-dragen-results --vcf_file examples/sample_001.vcf --metrics_file examples/sample_001.variant_metrics.csv
    --outdir was not specified and therefore was set to '/tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758'
    Created output directory '/tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758'
    --logfile was not specified and therefore was set to '/tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/analyze_dragen_output_results.log'
    --figure_file was not specified and therefore was set to '/tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/sample_001.quality_distribution.png'
    --variant_summary_report_file was not specified and therefore was set to
    '/tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/sample_001.variant_summary_report.txt'
    --metrics_summary_report_file was not specified and therefore was set to
    '/tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/sample_001.metrics_summary_report.txt'

Contents of the variant summary report file:

.. code-block:: shell

    cat /tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/sample_001.variant_summary_report.txt
    ## method-created: /tmp/test-dragen-results-utils/venv/lib/python3.10/site-packages/dragen_results_utils/analyzer.py
    ## date-created: 2025-02-27-171759
    ## created-by: sundaram
    ## vcf-file: /tmp/examples/sample_001.vcf
    ## metrics-file: /tmp/examples/sample_001.variant_metrics.csv
    ## logfile: /tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/analyze_dragen_output_results.log
    Total_Variants: 5
    Passed_Filters: 4
    Average_QUAL: 39.44

Contents of the metrics summary report file:

.. code-block:: shell

    cat /tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/sample_001.metrics_summary_report.txt
    ## method-created: /tmp/test-dragen-results-utils/venv/lib/python3.10/site-packages/dragen_results_utils/analyzer.py
    ## date-created: 2025-02-27-171759
    ## created-by: sundaram
    ## vcf-file: /tmp/examples/sample_001.vcf
    ## metrics-file: /tmp/examples/sample_001.variant_metrics.csv
    ## logfile: /tmp/dragen-results-utils/analyze_dragen_output_results/2025-02-27-171758/analyze_dragen_output_results.log
    METRIC: VALUE
    Total SNPs: 4.0
    Total Indels: 1.0
    Ti/Tv Ratio: 2.0
    Heterozygosity Rate: 0.6
    Variants Passing Filters: 4.0
    Mean Variant Quality: 39.44
