PCR Report Generation

Python project for automatic report generation from PCR measurements.

Configuration files

*_conc.csv

Sheet is used as look up table for sample indexing.

File shall contain sample_id, type,name, dilution where

• sample_id: integer, number of sample
• type: string, sample ty on of
  • nc: negative control
  • pc: plasmid control
  • s: sample
  • TODO: add if necessary, shall be added to the code!
• name: string, sample name
• dilution: float, final dilution

Prerequisities

To install python libraries use

pip install -r requirements.txt```

Install pandoc frpm pandoc website.

Install latex from any of the distributions.

Buld distribution of pcrep

For experts only!
To build a pcrep library execute following command:

python -m build --sdist --wheel

Running with exported csv data

This is a prefered way to run the prepcessing of the results followed by report generating. The script report_gen.py has two command line argumets --cfg CONFIG_PATHand CSV_PATH, where CONFIG_PATH is a path directory containing configuration files, and CSV_PATH is a file path of csv file from PCR analysis.

python report_gen.py --cfg C:/work/pcr-report/data C:/work/pcr-report/example/231108_GN004773-019/230811_GN004773-019_20230811_100101_999.csv

or using relative paths

python report_gen.py --cfg ./example/231108_GN004773-019/230811_GN004773-019_20230811_100101_999.csv

Check the data

Method check

Method check is applied to original device output data column Conc(copies/µL) using data from file ./data/method_limits.csv.

Number of droplets check

NUmber of droplets check is defined by minimum number of total droplets and is applied to column Accepted Droplets of the device original data.

Control limit checks

Controll limits checks are applied to reference rc and plasmid control pc. Column used for check is computed method result vg/ml.

Coefficient of variation (CV)

Is applied to multiple target PCR samples and controls, plasmid control pc and reference control rc.

Notes

• same units everywhere (SOP SOP-051000) [vg/μl]; excell [ml]
• look up tables: thinking in 'computer / programmer' way so that thinks could be indexed, automatically found (sample types, ...)
• CSV delimiter
• unify naming convention (lowercase/camelcase, separator, datetime format, ...)
• UNITS: compute in SOP and device units (shall be the same). Do units conversion at the very end for desired customer output.