pathogena 2.0.0rc1

The command line and Python client for EIT Pathogena

EIT Pathogena client

The command line interface for the EIT Pathogena mycobacterial platform. The client enables privacy-preserving sequence data submission and retrieval of analytical output files.

Prior to upload, sample identifiers are anonymised and human host sequences are removed. A multicore machine with 16GB of RAM running Linux or MacOS is recommended.

Install

Installing Miniconda

If a conda package manager is already installed, skip to Installing the client, otherwise:

Linux

• In a terminal console, install Miniconda, following instructions and accepting default options:

  curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  bash Miniconda3-latest-Linux-x86_64.sh
  

MacOS

The client requires an x86_64 conda installation. If your Mac has an Apple processor, disable or delete existing arm64 conda installations before continuing.

• If your Mac has an Apple processor, using Terminal, firstly run:

  arch -x86_64 zsh
  

• Install Miniconda using Terminal, following instructions and accepting default options:

  curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
  bash Miniconda3-latest-MacOSX-x86_64.sh
  

Installing or updating the client

• If using a Mac with an Apple processor, using Terminal, firstly run:

  arch -x86_64 zsh
  

• Perform the installation/upgrade:

  conda create -y -n pathogena -c conda-forge -c bioconda hostile==1.1.0
  conda activate pathogena
  pip install --upgrade pathogena
  

• Test:

  pathogena --version
  

Tab completion

Tab completion can optionally be enabled by adding the following lines to your shell source files. This will enable the ability to press tab after writing pathogena to list possible sub-commands. It can also be used for sub-command options, if -- is entered prior to pressing tab.

Example usage

Enabling tab completion

Run the following command and follow the output to enable autocompletion, this will need to be executed on every new shell session, instructions are provided on how to make this permanent depending on your environment. More information and instructions for other shells can be found in the Click documentation.

$ pathogena autocomplete
Run this command to enable autocompletion:
    eval "$(_PATHOGENA_COMPLETE=bash_source pathogena)"
Add this to your ~/.bashrc file to enable this permanently:
    command -v pathogena > /dev/null 2>&1 && eval "$(_PATHOGENA_COMPLETE=bash_source pathogena)"

Usage

Ensure that the conda environment is active:

conda activate pathogena

Help

Run pathogena --help for an overview of CLI subcommands. For help with a specific subcommand, use e.g. pathogena auth --help

Authentication (pathogena auth)

You will need to authenticate the first time you use the client. Do this by running pathogena auth and entering your username and password. A token will be saved automatically inside your home directory.

pathogena auth
Enter your username: [e-mail]
Enter your password: ***************

Uploading samples (pathogena upload)

The upload subcommand performs metadata validation and client-side removal of human reads for each of your samples, before uploading sequences to EIT Pathogena for analysis.

pathogena upload tests/data/illumina.csv

During upload, a mapping CSV is created (e.g. a5w2e8.mapping.csv) linking your local sample names with their randomly generated remote names. Keep this file safe, as it is useful for downloading and relinking results later.

A 4GB human genome index is downloaded the first time you run pathogena upload. If for any reason this is interrupted, simply run the upload command again. Upload will not proceed until the index has been downloaded and passed an integrity check. You may optionally download the index ahead of time using the command pathogena download-index.

To retain the decontaminated FASTQ files uploaded to EIT Pathogena, include the optional --save flag. To perform decontamination without uploading anything, use the pathogena decontaminate command.

Adding the --skip-fastq-check flag will prevent basic validity checks from being done on the contents of FASTQ files, saving time.

Downloading files (pathogena download)

The download subcommand retrieves the output (and/or input) files associated with a batch of samples given a mapping CSV generated during upload, or one or more sample GUIDs. When a mapping CSV is used, by default downloaded file names are prefixed with the sample names provided at upload. Otherwise downloaded files are prefixed with the sample GUID.

# Download the main reports for all samples in a5w2e8.mapping.csv
pathogena download a5w2e8.mapping.csv

# Download the main and speciation reports for all samples in a5w2e8.mapping.csv
pathogena download a5w2e8.mapping.csv --filenames main_report.json,speciation_report.json

# Download the main report for one sample
pathogena download 3bf7d6f9-c883-4273-adc0-93bb96a499f6

# Download the final assembly for one M. tuberculosis sample
pathogena download 3bf7d6f9-c883-4273-adc0-93bb96a499f6 --filenames final.fasta

# Download the main report for two samples
pathogena download 3bf7d6f9-c883-4273-adc0-93bb96a499f6,6f004868-096b-4587-9d50-b13e09d01882

# Save downloaded files to a specific directory
pathogena download a5w2e8.mapping.csv --out-dir results

# Download only input fastqs
pathogena download a5w2e8.mapping.csv --inputs --filenames ""

The complete list of --filenames available for download varies by sample, and can be found in the Downloads section of sample view pages in EIT Pathogena.

Generating Upload CSV (pathogena build-csv)

If you have a folder containing all the reads you would like to upload, then pathogena build-csv can be used to help generate the upload csv. See the Pathogena User Guide for detailed descriptions of all the fields. You'll need to fill in some of the required parameters.

pathogena build-csv --output-csv upload.csv --batch-name test_batch --collection-date 2024-04-15 --country GBR --max-batch-size 25 my_folder

You can then go through the csv and manually mark samples as positive/negative controls, or give them sample names (by default they are named based on the filename).

Querying sample metadata (pathogena query)

The query subcommand fetches either the processing status (pathogena query status) or raw metadata (pathogena query raw) of one more samples given a mapping CSV generated during upload, or one or more sample GUIDs.

# Query the processing status of all samples in a5w2e8.mapping.csv
pathogena query status a5w2e8.mapping.csv

# Query the processing status of a single sample
pathogena query status 3bf7d6f9-c883-4273-adc0-93bb96a499f6

# Query all available metadata in JSON format
pathogena query raw a5w2e8.mapping.csv

Downloading decontamination indexes (pathogena download-index)

The human genome index used for host decontamination is downloaded automatically when running pathogena upload for the first time. You may trigger this manually ahead of upload with pathogena download-index.

Support

For technical support, please open an issue or contact [e-mail]