openvax / topiary / 24469534512

88%

master: 90%

Build Type

Pull #136

github

Committed by iskandr

Commit Message

CachedPredictor: CLI support + real NetMHC fixtures + README reorder

## CLI

New `--mhc-cache-*` argument group lets users run topiary entirely
from pre-computed prediction files, without invoking a live MHC
predictor.  Every CachedPredictor loader has a CLI path:

  topiary --peptide-csv peptides.csv \
      --mhc-cache-file netmhcpan_run.out \
      --mhc-cache-format netmhcpan_stdout \
      --output-csv results.csv

Flags: --mhc-cache-file, --mhc-cache-directory (+ pattern),
--mhc-cache-format (8 choices), --mhc-cache-predictor-name /
--mhc-cache-predictor-version overrides, --mhc-cache-tsv-column
(repeatable), --mhc-cache-tsv-sep, plus format-specific mode and
version knobs for the NetMHC family.

--mhc-predictor / --mhc-alleles become optional when a cache is
supplying predictions.  A combined --mhc-cache-file +
--mhc-cache-directory raises; missing --mhc-cache-format with a
--mhc-cache-file raises; etc. — all validated with actionable
messages.

## Real NetMHC fixtures

tests/data/netmhc_fixtures/ now holds captured stdout from the
netmhc-bundle binaries for peptide SLLQHLIGL against HLA-A*02:01,
HLA-A*24:02, HLA-B*07:02 (substituted for B*07:01 which isn't in
NetMHCpan's allele list):

- netmhcpan-4.1 and 4.0 output (single-allele per file)
- netmhc-4.0 output (multi-allele works)
- netmhcstabpan output (single-allele)

Multi-allele NetMHCpan outputs are also committed but currently
don't parse through mhctools; filed as openvax/mhctools#195 with
the root-cause analysis (per-allele "Distance to training data"
header lines confuse the row parser).  NetMHCcons skipped because
the binary requires python2 which isn't on this machine's PATH.

## Tests

- 6 new TestRealNetMHCFixtures tests assert the actual numeric
  predictions (e.g. SLLQHLIGL × HLA-A*02:01 = 8.82 nM, 0.105%rank)
  parse through each from_*_stdout loader.
- 9 new tests in tests/test_cli_cached_predictor.py exercise the
  CLI end-to-end: error paths, happy paths for netmhcpan / net... (continued)

Pull Request Pull Request #136: CachedPredictor CLI + real NetMHC fixtures + README reorder

Coverage Stats

59 of 66 new or added lines in 3 files covered. (89.39%)

39 existing lines in 2 files now uncovered.

3368 of 3816 relevant lines covered (88.26%)

2.65 hits per line