previsedx-esopredict-qc-utils 0.5.2

Usage

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:

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:

 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  =====================================================================