mhctools
One Python interface to ~30 MHC binding, presentation, immunogenicity, and antigen-processing predictors.
Each predictor has its own input format, output format, allele spelling, and
installation ritual. mhctools gives them all the same predict() call and the
same result objects, so swapping NetMHCpan for MHCflurry is a one-line change
and comparing them is a DataFrame. Everything runs locally.
- Install and predict
- Core concepts
- Common tasks
- Predictor catalog
- Getting models
- Command line
- Beyond peptide-MHC
- Legacy API
- Further reading
Install and predict
pip install mhctools
Calis works immediately with no download. Most predictors need model weights
or an external tool first — see getting models. For
MHCflurry:
pip install mhcflurry
mhctools fetch mhcflurry
Then predict:
from mhctools import MHCflurry
predictor = MHCflurry(alleles=["HLA-A*02:01", "HLA-B*07:02"])
results = predictor.predict(["SIINFEKL", "GILGFVFTL"])
for r in results:
if r.affinity:
print(f"{r.peptide} -> {r.affinity.allele} IC50={r.affinity.value:.1f}nM")
That is the whole pattern. Every predictor in the catalog below is constructed
the same way and answers the same predict() call.
Core concepts
predict() returns a list of PeptideResult. Each one carries the peptide
string and gives you accessors for each kind of prediction. An accessor returns
None when the predictor doesn't produce that kind — so r.stability is
None from an affinity-only model, rather than an error or a zero.
Match results to inputs on
r.peptide, not by position. How many results you get back currently depends on the predictor. The NetMHC family andSMM/SMMPMBECreturn one result per distinct(peptide, offset, source_sequence_name), so a repeated peptide collapses into a single result and a peptide with no predictions is absent, whileMHCflurryandCalisreturn one per input occurrence.zip(peptides, results)is therefore not safe in general (#451).
r = results[0]
r.peptide # "SIINFEKL"
r.offset # position in source protein (if scanned)
r.kinds # {"pMHC_affinity", "pMHC_presentation", "antigen_processing"}
r.alleles # {"HLA-A*02:01", "HLA-B*07:02"}
# best prediction of each kind, or None when the kind is absent
r.affinity
r.presentation
r.stability
if r.affinity:
r.affinity.value # IC50 in nM
r.affinity.percentile_rank # 0-100, lower = better
r.affinity.score # predictor-specific scale, higher = better
r.affinity.allele # best allele for this kind
r.best_affinity_by_rank # by lowest percentile rank instead of score
r.preds # tuple of every underlying Prediction
r.filter(kind="pMHC_affinity")
r.filter(allele="HLA-A*02:01")
Underneath, each PeptideResult wraps a tuple of Prediction objects —
frozen dataclasses, one per allele-kind combination, each self-contained:
from mhctools import Prediction
pred = Prediction(
kind="pMHC_affinity",
score=0.85, # predictor-specific scale, higher = better
peptide="SIINFEKL",
allele="HLA-A*02:01",
value=120.5, # IC50 in nM
percentile_rank=0.8,
source_sequence_name="TP53",
offset=42,
predictor_name="netMHCpan",
predictor_version="4.1",
)
Three fields do most of the work, and they mean the same thing everywhere:
score— always present, always higher-is-better, but on a predictor-specific scale.value— a physical quantity on a linear scale, in that kind's canonical unit (nM for affinity, hours for stability). Empty when the kind has no unit, or when the wrapper cannot honestly convert to it.percentile_rank— 0-100, lower is stronger, present when the predictor scores against a background distribution.
A predictor can emit more than one kind. NetMHCpan 4.1, for example, produces
both pMHC_affinity and pMHC_presentation for every peptide-allele pair.
📖 Full reference: prediction kinds, units, and MHC context
— the 17 kinds, what fills value, how MeasurementContext works, and which
kind each predictor emits.
Common tasks
Scan proteins instead of peptides
predict_proteins() takes a dictionary of sequences and returns
{sequence_name: list[PeptideResult]}, with each result's offset set:
proteins = predictor.predict_proteins(
{"TP53": "MEEPQSDPSVEPPLSQETFS...", "KRAS": "MTEYKLVVVGAGGVGKS..."},
peptide_lengths=[9, 10],
)
for r in proteins["TP53"]:
if r.affinity and r.affinity.value < 500:
print(f" offset={r.offset} {r.peptide} IC50={r.affinity.value:.0f}")
Get a DataFrame
Every level has a _dataframe variant that flattens to a pandas DataFrame:
df = predictor.predict_dataframe(["SIINFEKL"], sample_name="pat001")
df = predictor.predict_proteins_dataframe({"TP53": "MEEPQ..."}, sample_name="pat001")
The columns are the same for every predictor:
| Column | |
|---|---|
sample_name |
who this was predicted for |
peptide, n_flank, c_flank |
the peptide and its flanking residues |
source_sequence_name, offset |
where it came from, if scanned |
predictor_name, predictor_version |
what produced it |
allele, tcr |
the MHC allele and/or TCR, empty when not applicable |
kind, score, value, percentile_rank |
the prediction itself |
measurement_context, peptide_input, cache_key |
assay context and exact-input identity |
Run many samples with different genotypes
from mhctools import MultiSample, MHCflurry
ms = MultiSample(
samples={
"pat001": ["HLA-A*02:01", "HLA-B*07:02"],
"pat002": ["HLA-A*01:01", "HLA-B*08:01"],
},
predictor_class=MHCflurry,
)
results = ms.predict(["SIINFEKL", "GILGFVFTL"]) # {sample: [PeptideResult]}
protein_results = ms.predict_proteins({"TP53": "MEEPQ..."}) # {sample: {seq: [...]}}
df = ms.predict_dataframe(["SIINFEKL"]) # flat, with sample_name
df = ms.predict_proteins_dataframe({"TP53": "MEEPQ..."})
Add predictor scores to an existing table
Evaluation workflows often start from an annotated benchmark table — columns
like sample_id, hit, peptide, and a per-row genotype — and just need
scores appended. annotate_table is I/O-free and works on any DataFrame:
from mhctools import annotate_table, AnnotationSpec, NetMHCpan42_BA
annotated = annotate_table(
df,
[AnnotationSpec(
predictor=lambda alleles: NetMHCpan42_BA(alleles=alleles),
output_column="netmhcpan4.2.ba",
field="affinity")],
peptide_column="peptide",
allele_column="hla")
There's a CLI equivalent that reads and writes CSV.
Predictor catalog
Start from what you want to know:
| I want to predict… | Kind | Predictors |
|---|---|---|
| Binding affinity to an allele | pMHC_affinity |
NetMHCpan, NetMHC, NetMHCIIpan, NetMHCcons, MHCflurry, CapHLA, SMM, SMMPMBEC |
| Surface presentation | pMHC_presentation |
NetMHCpan41/42, NetMHCIIpan, MHCflurry, CapHLA, MixMHCpred (I), MixMHC2pred (II), BigMHC |
| How long the pMHC complex lasts | pMHC_stability |
NetMHCstabpan |
| Combined antigen processing | antigen_processing |
MHCflurry |
| Proteasomal cleavage | proteasome_cleavage |
Pepsickle, NetChop, NetCleave_I |
| Endolysosomal cleavage (class II) | endolysosomal_cleavage |
NetCleave_II |
| TAP transport into the ER | tap_transport |
DeepTAP |
| ERAP1 N-terminal trimming | erap_trimming |
ERAMER |
| Whether a T cell responds | immunogenicity |
Calis, PRIME, BigMHC_IM, DeepImmuno, TLimmuno2 (II) |
| Whether a specific TCR recognises it | pMHC_TCR_binding |
NetTCR, Tulip, MixTCRpred |
| How long the free peptide survives | peptide_half_life |
PeptiVerse, PlifePred2 |
| Which peptidase cuts which bond | — | cleavage API |
📖 Predictor reference — what each model does, what it needs installed, and a worked example for every one.
⚠️ Known limits — several of these models are weaker than their own papers suggest. Worth reading before you trust a score.
RandomBindingPredictor is built in and produces random affinities, which is
occasionally useful as a null baseline.
Getting models
Most predictors need something downloaded first. There is one command for all of it:
mhctools ls # what exists, where it lives, who manages it
mhctools fetch mhcflurry # get it
mhctools predictors # can it actually run?
fetch is idempotent, so a provisioning script can call it over a whole list
without special-casing tools it cannot install. Where a predictor has its own
download manager, mhctools reports that manager's path instead of making a
second copy. Academic-licensed tools need an explicit --accept-license, and
the DTU NetMHC family needs a license you request from DTU directly.
from mhctools import MHCflurry, fetch, list_artifacts
MHCflurry.fetch()
for artifact in list_artifacts():
print(artifact.name, artifact.manager, artifact.version, artifact.path)
📖 Getting models — the full fetch/ls/predictors
reference, cache locations, the four ownership tiers, and licensing.
Command line
| Command | Does |
|---|---|
mhctools |
Predict for peptides or FASTA sequences |
mhctools ls |
List model artifacts and where they live |
mhctools fetch |
Download model weights and tool snapshots |
mhctools predictors |
Report which predictors can actually run |
mhctools predict-table |
Append predictor scores to a CSV |
mhctools cleavage |
Per-bond peptidase evidence |
mhctools vaccine-report |
Route-aware vaccine construct report |
mhctools benchmark |
Assay-aware model evaluation |
mhctools mixtcrpred |
Score paired TCRs against a fixed target |
Predict for peptides you supply
mhctools --sequence SIINFEKL SIINFEKLQ --mhc-predictor netmhc --mhc-alleles A0201
--sequence may be repeated and all occurrences accumulate. Or use
--input-peptides-file for one peptide per line (blank lines ignored), or
--input-fasta-file for protein sequences. Pick exactly one of the three.
Extract subsequences automatically
mhctools --sequence AAAQQQSIINFEKL --extract-subsequences \
--mhc-peptide-lengths 8-10 --mhc-predictor mhcflurry --mhc-alleles A0201
Annotate a table (predict-table)
Reads a CSV, runs each requested predictor once, and appends one score column per predictor — choosing the best allele per row — while preserving every input column:
mhctools predict-table \
--input benchmark.csv.bz2 \
--peptide-column peptide \
--alleles-column hla \
--predictor netmhcpan42-ba:netmhcpan4.2.ba:affinity \
--predictor netmhcpan42-el:netmhcpan4.2.el:score \
--out benchmark.with_scores.csv.bz2
Each --predictor spec is NAME[:OUTPUT_COLUMN[:FIELD]], where FIELD is
affinity, score, or percentile_rank. Lower is better for affinity and
percentile_rank, higher for score.
A row may hold several alleles per cell (whitespace-, comma-, or
semicolon-separated); the best one per peptide is chosen and recorded in a
<OUTPUT_COLUMN>_best_allele provenance column. Missing or blank
peptide/allele cells stay unscored — they are never coerced into a literal
sequence or allele string and sent to a predictor.
Pass --predictor-info info.csv to also write a sidecar describing each
column's score_field, units, and higher_is_better. Empty units means
the field is dimensionless or predictor-specific.
Output conventions
CLI prediction tables follow one convention across every predictor. Plain
peptide inputs get an empty source_sequence_name and offset 0, while FASTA
and subsequence inputs keep their source and zero-based offset and are ordered
by those coordinates. prediction_method_name is the exact CLI predictor name
you selected, including version and mode. affinity is IC50 in nM,
percentile_rank is a 0–100 percentile, and score stays
predictor-specific. CSV floats are serialized with six significant digits.
Default stdout is streamed as tab-separated values, so an empty source name
survives as an empty field and large tables don't need a second formatted copy
in memory. A downstream closed pipe (| head, say) exits cleanly.
Beyond peptide-MHC
Three features that don't fit the peptide-in, score-out shape:
Per-bond peptidase evidence. DPP4qPISA evaluates the
published human DPP4 N-terminal triplet model locally. CleavageInput and
CleavageResult preserve terminal chemistry, native scores, assay provenance,
and parent-sequence bond coordinates. The panel also provides motif rules for
CPN, aminopeptidase P, FAP, aminopeptidases A/N, DPP8/9, TPP2,
puromycin-sensitive aminopeptidase, PREP, and ERAP2, each stating how strict it
is (required, preferred, or permissive) together with the source
observation behind that grade — so a non-match can be read for what it is
worth. Three enzymes whose published specificity does not generalize (THOP1,
neurolysin, endosomal IRAP) ship as exact-sequence source references instead:
they report what an experiment found for that precise chemical form and abstain
on anything else.
An optional eramer-step model exposes ERAP1's existing length-specific PWM
score at the initial trimming bond. Installed Pepsickle epitope models are
available through the same per-bond contract, with exact weight,
inference-code, and feature-code hashes; their forced endpoint zero is excluded
rather than mislabeled as an internal bond.
mhctools cleavage --list-models
mhctools cleavage --sequence RPPGFSPFR --model app2-xp --model cpn-basic
The cleavage guide also carries a wider candidate inventory and prioritized follow-up issues. qPISA scores are substrate-depletion estimates, not serum half-lives or probabilities.
Route-aware vaccine reports. mhctools vaccine-report reads a structured construct manifest and writes a timestamped
directory containing a sequence-centered PDF, declared processing-route policy,
selected MHC windows, placement assessments, and checksums:
mhctools vaccine-report \
--input docs/vaccine-report-example.json \
--output-dir vaccine-reports
Injected SLP and RNA-encoded constructs use different route policies. Cytosolic RNA emphasizes proteasome/ER/class-I processing and omits free serum-peptide tracks; an injected SLP begins extracellularly/endolysosomally while retaining proteasome/TAP cross-presentation as a conditional route.
Assay-aware benchmarks. mhctools benchmark
evaluates source-linked observations in separate assay, endpoint, and
native-unit strata, reporting training overlap, repeated measurements,
unsupported inputs, and missing target-domain evidence. See also mhctools benchmark --lineage-inventory.
Legacy API
The old predict_peptides() and predict_subsequences() methods still work
and return BindingPredictionCollection objects:
predictor = NetMHCpan(alleles=["A*02:01"])
collection = predictor.predict_subsequences(
{"1L2Y": "NLYIQWLKDGGPSSGRPPPS"},
peptide_lengths=[9],
)
df = collection.to_dataframe()
for bp in collection:
if bp.affinity < 100:
print("Strong binder: %s" % bp)
To convert legacy results to the new types:
preds = collection.to_preds() # list of Prediction
pp_list = collection.to_peptide_preds() # list of PeptideResult
The historical Iedb* predictor names also still work, as local wrappers — see
compatibility names.
Further reading
| Guide | Covers |
|---|---|
| Prediction kinds | The 17 kinds, units, MeasurementContext, MHC dependence |
| Predictor reference | Per-predictor setup and examples |
| Known limits | Every caveat, collected and indexed |
| Getting models | fetch, ls, predictors, caches, licensing |
| Cleavage evidence | Per-bond peptidase API and model panel |
| Vaccine reports | Input schema, route policies, Vaxrank integration |
| Benchmarks | Assay-aware evaluation and training-overlap reporting |
| Peptide PK and uptake | Half-life, clearance, uptake, tissue exposure |
| Optional backend conformance | Artifact verification and capability levels |
| Testing | Running the full suite, optional model setup, CI |
Development
./develop.sh # editable install
./lint.sh # ruff
./test.sh # pytest
For a complete run with no skipped tests, and for setting up the optional predictor backends, see the testing guide. Releases are described in RELEASING.md.
5 maintainers
Release files for mhctools 3.44.57
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
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|---|---|---|---|
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Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| mhctools-3.44.57-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 800.9 kB
Release files / mhctools-3.44.57.tar.gz
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