Getting started#

Install#

bash setup.sh            # repo-local .venv + editable install (uses sibling ../seqtree if present)
bash setup.sh --tests    # + pytest
bash setup.sh --logo     # + logomaker/matplotlib for rendering logos

Quickstart#

import mhcmatch

# build from the isalgo/pmhc_data table (full or shortlist tier)
store = mhcmatch.Store.from_pmhc("pmhc_full.tsv.gz", species="human")

store.restriction("NLVPMVATV")                 # ranked presenting alleles + binder flags
store.is_binder("NLVPMVATV", "HLA-A*02:01")
store.scan_protein(my_protein, cls="mhc1")      # presented peptides in a protein
store.decompose("NLVPMVATV", cls="mhc1")        # (tcr_facing, presentation) with X masks

# similarity at scale
mhcmatch.search.search("NLVPMVATV", big_peptide_set, mode="tcr")
mhcmatch.search.find_mimics("EAAGIGILTV", self_set, bacterial_sets={...})

# near-exact source of a neoantigen
pm = mhcmatch.Proteome.from_fasta("UP000005640_9606.fasta.gz")
pm.find_source("NLVPMVATV", max_subs=1)

# diffusion-powered forward scorer (rescues rare alleles)
am = store.anchor_model("mhc1")
am.score("NLVPMVATV", "HLA-A*02:01")            # am.score(..., raw=True) disables borrowing

Data#

  • Reference ligands — isalgo/pmhc_data (full / shortlist tiers); pass the path to mhcmatch.Store.from_pmhc() or set MHCMATCH_PMHC.

  • Pseudosequences — 34-mer groove pseudosequences vendored in src/mhcmatch/data/.

  • Reference proteomes — supply a UniProt reference proteome FASTA to mhcmatch.Proteome.from_fasta() (not bundled).