previsedx-esopredict-qc-utils 0.5.2
Collection of software for QC checks for PreviseDx Esopredict.
Requires Python: >=3.10
Keywords: previsedx_esopredict_qc_utils

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esopredict-qc-utils
===================


Collection of software for QC checks for esopredict


Usage
-----

.. code-block:: python

    from esopredict-qc-utils import Manager as QCManager

    config_file = "conf/config.yaml"
    config = yaml.safe_load(Path(config_file).read_text())

    manager = QCManager(
        config=config,
        config_file=config_file,
        indir=indir,
        infile=infile,
        logfile=logfile,
        outdir=outdir,
        outfile=outfile,
        verbose=verbose,
    )

    manager.run_qc_checks()

Exported console script
------------------------

To use the exported script for running QC checks:

.. code-block:: bash

    run-esopredict-qc-checks --indir /tmp/demo/ID24-0114 --infile /tmp/demo/ID24-0114/ANA-FOR-001-F2_Analysis_Risk_Algorithm_V6.0_ID24-0114.tsv --outdir .
    --config_file was not specified and therefore was set to '/tmp/previsedx-esopredict-qc-utils/venv/lib/python3.10/site-packages/previsedx_esopredict_qc_utils/conf/config.yaml'
    --logfile was not specified and therefore was set to './run_esopredict_qc_checks.log'
    --outfile was not specified and therefore was set to './run_esopredict_qc_checks.qc-checks-report.txt'

Excerpt of QC report file:

.. code-block:: text

     1  ## method-created: /tmp/previsedx-esopredict-qc-utils/venv/lib/python3.10/site-packages/previsedx_esopredict_qc_utils/qc/reporter.py
     2  ## date-created: 2025-02-15-082341
     3  ## created-by: sundaram
     4  ## config_file: /tmp/previsedx-esopredict-qc-utils/venv/lib/python3.10/site-packages/previsedx_esopredict_qc_utils/conf/config.yaml
     5  ## indir: /tmp/demo/ID24-0114
     6  ## logfile: ./run_esopredict_qc_checks.log
     7  Summary
     8  ========
     9  
    10  (1): Standard Curve QC checks - PASS
    11          See section 2 'Standard Curve QC' in SOP document ANA-FOR-001-F1-Analysis_QC_5.0.pdf
    12  
    13  (2): Standards Dilution checks - PASS
    14          See section 1 'Run Check' SOP document ANA-FOR-001-F1-Analysis_QC_5.0.pdf
    15  
    16  (3): NEG QC checks - FAIL
    17          See section 4 'Controls Criteria Table' in SOP document of ANA-FOR-001-F1-Analysis_QC_5.0.pdf
    18  
    19  (4): NTC QC checks - PASS
    20          See section 4 'Controls Criteria Table' in SOP document of ANA-FOR-001-F1-Analysis_QC_5.0.pdf
    21  
    22  (5): EXT QC checks - PASS
    23          See section 4 'Controls Criteria Table' in SOP document of ANA-FOR-001-F1-Analysis_QC_5.0.pdf
    24  
    25  (6): POS-High QC checks - PASS
    26          See section 4 'Controls Criteria Table' in SOP document of ANA-FOR-001-F1-Analysis_QC_5.0.pdf
    27  
    28  (7): Sample QC beta-Actin Quantity QC checks - PASS
    29          See section 5 'Sample QC (0.0016 < b-Actin < 1.000)' in SOP document of ANA-FOR-001-F1-Analysis_QC_5.0.pdf
    30  
    31  
    32  Details
    33  ========
    34  
    35  =====================================================================
    36  # Check Category Number: 1
    37  # Check Name: Standard Curve QC checks
    38  # Description: See section 2 'Standard Curve QC' in SOP document ANA-FOR-001-F1-Analysis_QC_5.0.pdf
    39  # Overall Status: PASS
    40  =====================================================================


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History
=======

0.1.0 (2024-09-06)
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* First release on PyPI.