PBEST-Docker

This repository contains a Docker image of PBEST, used to screen COVID-19 samples via group testing, as described in the manuscript "Efficient high throughput SARS-CoV-2 testing to detect asymptomatic carriers", by Shental et al.

The PBEST protocol allows screening 384 samples using 48 pools, where each sample appears in six pools according to a Reed-Solomon error-correcting code.

PBEST-Docker allows you to analyze experimental results and detect positive carriers.

Please visit the links above for more details about PBEST and how make the pooling

Requirements

You need docker-engine

See docker docs

Quickstart

The first execution could require several minutes, from the second one will be faster.

Clone the repository:

$ git clone https://github.com/next-crs4/PBEST-Docker

Cd into the docker directory:

$ cd PBEST-Docker

Using the Makefile

Print the help message

$ make help

Please use `make <target>` where <target> is one of
  build                   build the pbest image
  clean                   remove the pbest image from your computer

Build the PBEST image

$ make build

If successfully built:

Successfully built 5ae8a1ad8216 
Successfully tagged pbest:Dockerfile

Ready to start. Try:
        pbest --help
        pbest-test --help

List all the locally stored Docker images

$ docker images

REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
pbest               Dockerfile          5ae8a1ad8216        24 minutes ago      1.88GB
python              3                   7f5b6ccd03e9        13 days ago         934MB

PBEST script

Starting from experimental results, pbest script detect positive carriers.

Print the help message

$ pbest --help

usage: pbest [-h] --input-file FILE --output-file FILE [--output-format STR]
             [--force] [--logfile PATH]

Run PBEST algorithm to identify COVID-19 positive carriers

optional arguments:
  -h, --help            show this help message and exit
  --input-file FILE, -i FILE
                        input file (experimental results)
  --output-file FILE, -o FILE
                        output file (detected samples)
  --output-format STR, -t STR
                        Output file format: [tsv,csv,xlsx]
  --force, -f           force to overwrite output file
  --logfile PATH        log file (default=stderr)

An example of input-file .xlsx can be found here. Each row represents a pool: the first column identifies the pool, the second is a flag equals to '1' if the pool contains an unknown positive In this example, there are 12 pool set to '1': 6,8,15,20,21,27,31,32,34,39,41,46

Put this file in a local folder: /path/to/local/data/ExpTwoCarriersResults.xlsx Now, run the pbest script

$ pbest -i /path/to/local/data/ExpTwoCarriersResults.xlsx -o /path/to/local/data/DetectedSamples.xlsx

In this examples, the detected samples are [72, 142]. The related output-file .xlsx can be found here.

Use -f option to overwrite output file and -t to choose an other format (.csv or .tsv)

PBEST-TEST script

It tests the robustness and reliability of the pbest script, creating a dummy input-file with know positive carriers.

Print the help message

$ pbest-test --help

usage: pbest-test [-h] {random,select} ...

create dummy .xlsx files and test it

positional arguments:
  {random,select}

optional arguments:
  -h, --help       show this help message and exit

Random

$ pbest-test random --help

usage: pbest-test random [-h] --number INTEGER --output-file FILE [--force]
                         [--run] [--logfile PATH]

optional arguments:
  -h, --help            show this help message and exit
  --number INTEGER, -n INTEGER
                        number of asymptomatic carriers to be created
  --output-file FILE, -o FILE
                        output xlsx file
  --force, -f           force to overwrite output file
  --run, -r             run pbest script
  --logfile PATH        log file (default=stderr

Example: create a dummy file with 3 positive carrier (random)

$ pbest-test random -n 3 -o /path/to/local/data/Random3Carriers.xlsx -r

....
2020-06-23 15:32:13|INFO    |pBestTest |Carriers: [192, 218, 311]
2020-06-23 15:32:13|INFO    |pBestTest |Detected Samples: [192, 218, 311]
2020-06-23 15:32:13|INFO    |pBestTest |Testing successful!!!

Select

$ pbest-test select --help

usage: pbest-test select [-h] --carriers INT [INT ...] --output-file FILE
                         [--force] [--run] [--logfile PATH]

optional arguments:
  -h, --help            show this help message and exit
  --carriers INT [INT ...], -c INT [INT ...]
                        list of asymptomatic carriers to be created
  --output-file FILE, -o FILE
                        output xlsx file
  --force, -f           force to overwrite output file
  --run, -r             run pbest script
  --logfile PATH        log file (default=stderr)

Example: create a dummy file with 3 positive carrier on you choose

$  pbest-test select -c 35 187 261 -o /path/to/local/data/Selected3Carriers.xlsx  -r

....
2020-06-23 15:46:08|INFO    |pBestTest |Carriers: [35, 187, 261]
2020-06-23 15:46:08|INFO    |pBestTest |Detected Samples: [35, 187, 261]
2020-06-23 15:46:08|INFO    |pBestTest |Testing successful!!!

Finishing

Remove PBEST images from local computer

$ make clean