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Since this script can be long-running (due to the astoundingly slow netmhcpan), it should be possible to run it with a "--resume" flag that reuses partial outputs from a previous interrupted invocatio…
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Instead of invoking netMHCpan for every peptide/allele pairs, combine all the peptides into a single input file and then split them up afterward. Will be significantly faster.
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Allow option for using local models instead of calling to IEDB