ct2vl: C_t values to viral loads

A python package and command line tool to convert SARS-CoV-2 PCR C_t values to viral loads.

Installation

Assuming python and pip are installed, at the command line, run

pip install ct2vl

Usage

Python package

from ct2vl.conversion import Converter
converter = Converter(traces="traces.csv", LoD=100.0, Ct_at_LoD=37.96)
ct_values = [23.1, 31.8, 28.4, 34.0, 30.2]
viral_loads = converter.ct_to_viral_load(ct_values)

In addition to a filepath, the traces argument of Converter can also accept a pandas DataFrame or numpy ndarray.

Command line tool

To calibrate ct2vl run

python3 -m ct2vl calibrate <traces> <LoD> <Ct_at_LoD>

For example

python3 -m ct2vl calibrate example/path/traces.csv 100.0 37.96

Once ct2vl has been calibrated, C_t values can be converted to viral loads with

python3 -m ct2vl convert <Ct>

One or multiple C_t values can be passed. For example

python3 -m ct2vl convert 23.1

or

python3 -m ct2vl convert 23.1 31.8 28.4 34.0 30.2

Output can be saved to a file by providing a filepath to the optional flag --output

python3 -m ct2vl convert 23.1 --output example/path/viral_loads.tsv

Descriptions of command line arguments

The command line tool has two modes calibrate and convert.

• mode: calibrate uses positive PCR traces and their corresponding C_t values to calibrate ct2vl for a given machine
  1. traces: Filepath to a csv file containing PCR reaction traces
  2. LoD: Limit of detection (LoD): copies of SARS-CoV-2 viral genomes/mL (copies/mL; viral load at the LoD)
  3. Ct_at_LoD: C_t value at the limit of detection (LoD)
• mode: convert calculates the viral loads for given C_t values
  1. Ct: A list of C_t values that will be converted to viral loads
  2. --outfile: An optional filepath to save the results to

For calibrate mode, traces is a csv file where each row corresponds to a PCR reaction curve and each column is a cycle in the reaction (example below).

Example traces csv file

This file is available for download here. Each row is a PCR reaction curve for a given covid test and each column is a cycle in the PCR reaction.

Example command line output

Fine details

If you use conda: This package is currently only available from PyPI; however, using pip with conda is not really recommended, and conda skeleton requires a setup.py (the deprecated way of doing things). This recipe for installing in a conda environment seems to work:

conda install -c conda-forge grayskull
grayskull pypi ct2vl
cd ct2vl
conda build .
cd ..
conda install --use-local ct2vl

That being said, if you have suggestions or feedback on how to support conda installation, let us know.