feat: script to annotate proteome hits onto winnow outputs

[JemmaLDaniel]

Summary

Adds a post-winnow predict utility that annotates prediction outputs with a proteome_hit column by matching peptides against a reference FASTA proteome.

The script drops short peptides (default: fewer than 7 tokeniser residues), strips modifications and normalises I/L for matching, then uses Aho–Corasick substring search. It updates preds_and_fdr_metrics.csv in place and filters metadata.csv to the retained spectra. No changes to the Winnow CLI or library predict/train paths.

Adds pyahocorasick as a dependency.

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
__init__.py	0	0	100%
data_types.py	4	0	100%
calibration
__init__.py	0	0	100%
calibration_features.py	9	0	100%
calibrator.py	102	11	89%	69–70, 72, 107, 134–135, 137, 163, 168, 195–196
diagnostics.py	168	50	70%	70, 96, 101, 111, 115, 137, 146, 203–218, 261–262, 266, 307, 309–324, 335–341
calibration/features
__init__.py	10	0	100%
base.py	8	0	100%
beam.py	47	0	100%
chimeric.py	82	1	98%	213
constants.py	9	0	100%
fragment_match.py	78	1	98%	203
mass_error.py	67	2	97%	16, 20
retention_time.py	135	9	93%	183, 190, 206, 257–259, 269, 272–273
sequence.py	19	0	100%
token_score.py	37	1	97%	82
utils.py	261	3	98%	96, 368, 594
compat
__init__.py	0	0	100%
instanovo.py	10	6	40%	12, 14–15, 17, 24–25
datasets
__init__.py	0	0	100%
calibration_dataset.py	109	17	84%	155, 169, 171, 173, 183, 196, 249, 251–252, 258–261, 263–266
interfaces.py	3	0	100%
psm_dataset.py	25	0	100%
datasets/data_loaders
__init__.py	5	0	100%
instanovo.py	119	19	84%	90, 93, 119, 142, 168–169, 172–174, 176–177, 179, 182–183, 185, 343–345, 356
mztab.py	215	55	74%	103, 106, 157, 161, 210–211, 223, 236–240, 287, 290, 302–303, 315–317, 319–320, 322, 324, 330, 334–336, 338–339, 343–346, 350, 514–515, 518, 521, 528, 542–546, 550–555, 561, 570–571, 573, 599
pointnovo.py	7	0	100%
utils.py	59	1	98%	11
winnow.py	39	4	89%	54–55, 91–92
fdr
__init__.py	0	0	100%
base.py	58	15	74%	81, 85–86, 91, 98–99, 105, 126, 129–130, 135, 137–138, 144, 186
database_grounded.py	28	1	96%	52
nonparametric.py	25	4	84%	62, 68–69, 72
scripts
__init__.py	0	0	100%
annotate_proteome_hits.py	146	70	52%	41–43, 48–50, 52–57, 63, 73, 78, 82, 105, 107, 109, 111, 114, 117–118, 154–160, 162–166, 168–170, 173–174, 176–180, 182–184, 200–203, 208, 213–218, 221, 260, 266–267, 272–273, 275–277, 283, 289
main.py	256	256	0%	8, 10–13, 16–20, 23–24, 26–28, 32, 39, 44, 47, 53, 55–56, 59, 68, 76, 79, 86, 88–90, 92, 94–99, 102, 104–105, 110, 125, 128, 135–141, 144–145, 148, 161–163, 166, 169, 174, 176–178, 180, 182–183, 186–187, 190, 192–193, 195, 197, 199–200, 202, 205–206, 209–210, 213–214, 217–219, 221–224, 227–229, 231, 234, 248–250, 252, 254, 259, 261–263, 265–266, 268, 270–271, 273–275, 277, 279, 281–282, 286–289, 291–292, 294–295, 297–298, 300, 303, 317–319, 322, 325, 330, 332–334, 336–338, 340–341, 344–345, 348, 350–351, 353, 355, 357–358, 360, 363–364, 370–372, 374–377, 380–381, 384–385, 388–389, 392–393, 401–403, 407, 410, 414, 417, 423–425, 427–428, 435–436, 438, 440, 445, 447–449, 451–452, 455, 457–458, 460–463, 465–466, 468–469, 471–473, 479–480, 484–485, 488, 495, 500–501, 506–508, 511, 516, 526, 533, 535, 539, 541–542, 546–547, 550, 573, 586–587, 590, 612, 624–625, 628, 653, 666–667, 670, 685, 697–698, 701, 716, 728–729, 732, 744, 756–757, 760, 775, 787–788, 791, 800, 812–813
utils
__init__.py	4	0	100%
config_formatter.py	53	40	24%	29, 37–38, 40–42, 44, 55, 58–60, 62–63, 66–69, 72–74, 77–78, 80, 91, 102, 113, 127–128, 130–132, 145–147, 150, 153–154, 157–158, 160
config_path.py	76	5	93%	24–26, 117–118
peptide.py	16	0	100%
TOTAL	2289	571	75%

Tests	Skipped	Failures	Errors	Time
432	0 💤	0 ❌	0 🔥	39.585s ⏱️