The Multimer Validation Tool is a tool designed to validate multimers according to the MIAMM standard.
As a preliminary step, please download or clone the Git repository and go to the directory with the repository.
git clone https://github.com/IEDB/tetramer-validator.git cd tetramer-validator
If you would just like to run the validator tool by passing in the filename with the data on the command line, install using command
pip install .
tv -h to ensure installation and generate a usage message.
The above steps for installation ensures you can run the validator on the command line interface by passing in a filename with the data on multimers.
To get a local web server going, first follow the steps above to install the command line interface. Then install Flask.
Please enter the following command to install and run the Flask server locally.
pip install -r requirements.txt tv webserver
If you would like additional options for local web deployment, please consult the usage message.
If you wish to run the validator in a Docker container, please use the Dockerfile from the Git repo to build the image.
Please enter the following command to build the Docker image and run the Docker container.
docker build -t mhcmultimer:latest . docker run -p 5000:5000 mhcmultimer:latest
The tool allows you to run command line validation on a table of MHC Multimer entries that is saved as Excel Spreadsheet (
.xlsx), a tab-separated file (
.tsv), or a comma-separated file (
The following is the usage message for running command line validation.
usage: tv cmd_line [-h] [-o OUTPUT] filename positional arguments: filename Please enter .tsv, .csv, or .xlsx filename and that the following is in the header row: Peptide Sequence, Modification Type, Modification Position, MHC Molecule optional arguments: -h, --help show this help message and exit -o OUTPUT, --output OUTPUT Enter output file text name.
In order to assist user, the MHC Molecule and Modification Type fields output suggestions that conform to MHC Restriction ontology and PSI-MOD ontology, respectively. Please use the suggested names to ensure successful validation.
usage: tv webserver [-h] [--host HOST] [--port PORT] [--debug] optional arguments: -h, --help show this help message and exit --host HOST If this option is not specified, host will default to 127.0.0.1 --port PORT If this option is not specified, port will default to 5000 --debug Option used to specify if Flask server should start in debug mode
See below for an example on entering an entry into the web form.