pVACcompare is a file comparison suite built for comparing results generated by pVACtools. Comparison can be specified for MHC Class I results, MHC Class II results, or both. In its current state the following files are included in the comparison:
- log/inputs.yml
- all_epitopes.tsv
- all_epitopes.aggregated.tsv
- all_epitopes.aggregated.tsv.reference_matches
- all_epitopes.aggregated.metrics.json (inputs only)
pVACcompare is written for Linux, other operating systems have not been tested. pVACcompare requires Python 3.10 or above. Older versions may work, but have not been tested.
The following packages can be installed with pip and are required to run pVACcompare:
- deepdiff, yaml, pandas, numpy
pVACcompare offers several parameters that allow the user to have control of the comparisons.
Running the following in the terminal will display the help menu with all of the available parameters and options:
python3 run.py -h
An example of running the tool likes like the following:
python3 run.py --pvactools_release --mhc_class 1 --aggregated_columns 'Best Peptide', 'Best Transcript' version1/result version2/result differences
Note: You must specify if the results are from pVACtools or the Immuno pipeline. All columns specified must be in quotes and comma separated. If you do not specify MHC Class, the tool will include both in the report. A list of available columns is displayed in the help menu.
The above command will perform a MHC Class I output comparison between two result folders generated by pVACtools only with the specified columns included in the aggregated tsv comparison. Columns for the unaggregated tsv comparison and reference match tsv comparison were not specified, so the default columns will be used. The report will be generated in a differences_MHC_Class_I.tsv file.