IEDB Next-Generation Tools Mutated Peptide Generator - version TOOL_VERSION ======================================================================= Introduction ------------ The Mutant Peptide Generator tool will take a two-sample, SNPEff-annotated VCF as input and generate predicted neo-peptides and the reference / WT peptides with which they pair. Release Notes ------------- vTOOL_VERSION - Initial public beta release Prerequisites ------------- The following prerequisites must be met before installing this tool: + Linux or MacOS 64-bit environment + Python 3.10 or higher * http://www.python.org/ + Docker * https://docs.docker.com/engine/install/ + User with permission to execute docker commands Installation ------------ Below, we will use the example of installing an 'iedb_tools' folder inside your home directory. Replace '~/iedb_tools' with your desired target directory. 1. Extract the code and change directory: $ mkdir ~/iedb_tools $ tar -xvzf IEDB_NG_MPG-TOOL_VERSION.tar.gz -C ~/iedb_tools $ cd ~/iedb_tools/ng_mpg-TOOL_VERSION 2. Optionally, create and activate a Python 3.10+ virtual environment using your favorite virtual environment manager. Here, we will assume the virtualenv is at ~/virtualenvs/ng_mpg: $ python3 -m venv ~/venvs/ng_mpg $ source ~/venvs/ng_mpg/bin/activate 3. Install python requirements: $ python3 -m pip install --upgrade pip $ pip install -r requirements.txt Usage ----- python3 src/run_mutgen.py -j --output-directory The format of the input JSON file is described below. The result will saved to result.json file inside output_directory Input formats ------------- Currently, only JSON input is supported. *NOTE*: This tool only accepts JSON inputs, formatted as described below { "peptide_length": 21, "reference_genome": "GRCh38", "frameshift_overlap": 9, "maximum_peptide_length": 23, "peptide_mutation_position1": 11, "input_vcf": "examples/syntheticX.speedseq.ann.vcf" } More information on the individual parameters can be found at: https://nextgen-tools.iedb.org/docs/tools/mpg/index.html Output format ------------- The output file is also in JSON format. The 'results' section contains 3 output tables 'unique_peptide', 'peptide', and 'snp'. The tables are divided into a section of column headers, called 'table_columns' and the actual data, called 'table_data'. More information on these outputs can be found at: https://nextgen-tools.iedb.org/docs/tools/mpg/index.html Additional output formats and information on usage with 'pandas' will be included in a future release. In addition to the main output file, a log file is also included that may be useful for debugging. Caveats ------- All IEDB next-generation standalones have been developed with the primary focus of supporting the website. Some user-facing features may be lacking, but will be improved as these tools mature. Contact ------- Please contact us with any issues encountered or questions about the software through any of the channels listed below. IEDB Help Desk: https://help.iedb.org/ Email: help@iedb.org