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