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ct2vl-1.0.4
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مشاهده بیشترتوضیحات
Converting SARS-CoV-2 PCR test Ct values to viral loads
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | ct2vl-1.0.4 |
| نام | ct2vl |
| نسخه کتابخانه | 1.0.4 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Elliot Hill, Ramy Arnaout, Cody Callahan |
| ایمیل نویسنده | rarnaout@bidmc.harvar.edu |
| آدرس صفحه اصلی | https://github.com/Elliot-D-Hill/ct2vl |
| آدرس اینترنتی | https://pypi.org/project/ct2vl/ |
| مجوز | - |
# ct2vl: C<sub>t</sub> values to viral loads
A python package and command line tool to convert SARS-CoV-2 PCR C<sub>t</sub> values to viral loads.
## Installation
Assuming python and pip are installed, at the command line, run
pip install ct2vl
## Usage
### Python package
```python
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<sub>t</sub> values can be converted to viral loads with
python3 -m ct2vl convert <Ct>
One or multiple C<sub>t</sub> 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<sub>t</sub> 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<sub>t</sub> value at the limit of detection (LoD)
* `mode`: `convert` calculates the viral loads for given C<sub>t</sub> values
1. `Ct`: A list of C<sub>t</sub> 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](https://gist.github.com/Elliot-D-Hill/1ef5b826d23ffd6f29397958ca23eb7b). Each row is a PCR reaction curve for a given covid test and each column is a cycle in the PCR reaction.
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## Example command line output
| | LoD | Ct_at_LoD | Ct | viral_load | log10_viral_load |
| ---: | ---: | --------: | ----: | ----------: | ---------------: |
| 1 | 100 | 37.83 | 14.73 | 3.3277e+08 | 8.52214 |
| 2 | 100 | 37.83 | 20.27 | 7.98283e+06 | 6.90216 |
| 3 | 100 | 37.83 | 18.21 | 3.13511e+07 | 7.49625 |
| 4 | 100 | 37.83 | 18.05 | 3.48959e+07 | 7.54277 |
| 5 | 100 | 37.83 | 15.53 | 1.92109e+08 | 8.28355 |
## 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.
نیازمندی
| مقدار | نام |
|---|---|
| >=1.3.0 | pandas |
| >=1.21.5 | numpy |
| >=1.7.0 | scipy |
| >=1.0.2 | scikit-learn |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.7 | Python |
نحوه نصب
نصب پکیج whl ct2vl-1.0.4:
pip install ct2vl-1.0.4.whl
نصب پکیج tar.gz ct2vl-1.0.4:
pip install ct2vl-1.0.4.tar.gz