aadr-resolve 0.4.0

AADR cross-version GeneticID / MasterID join utility for ancient-DNA / population-genetics workflows.

aadr-resolve

AADR cross-version GeneticID / MasterID join utility for ancient-DNA and population-genetics workflows.

aadr-resolve reads AADR (Allen Ancient DNA Resource) .anno files across one or more releases and resolves the cross-version sample-ID join through the Master ID column — the part every ancient-DNA pipeline currently re-implements with custom awk. It handles AADR's progressive de-anonymization (I0001 in v44.3 → Loschbour.AG in v66) and the periodic Master-ID renames (9-18 per consecutive version pair; ~62 cumulative v44.3 → v66.0) automatically.

Designed and bench-verified against AADR releases v44.3, v50.0, v52.2, v54.1, v62.0, and v66.0; six schema classes (A–F) are recognized out-of-the-box via in-package YAML header signatures.

Install

pip install aadr-resolve

Requires Python 3.11+ and pip 23+ with setuptools 61+. If you are on a system Python (Ubuntu 22.04 ships pip 22 / setuptools 59), upgrade first:

python3.11 -m venv .venv && source .venv/bin/activate
pip install --upgrade pip   # brings pip to 23+, which upgrades setuptools automatically
pip install aadr-resolve

Installing without upgrading pip on older toolchains causes the package to appear as UNKNOWN 0.0.0, which breaks co-installation with other packages (see #3).

Dependencies: pandas 2.x, click 8.x, PyYAML 6.x.

Quickstart

Resolve a single sample across two AADR releases.

aadr-resolve lookup I0001 \
    --anno-files v44.3_1240K_public.anno \
    --anno-files v66.0_1240K_public.anno

Output (stdout):

query: I0001
canonical individual_id: Loschbour    (matched via individual_id)
v44.3 rows: 1
  I0001  Luxembourg_Loschbour  537,182 SNPs
v66.0 rows: 2
  Loschbour.AG  Luxembourg_Mesolithic.AG  155,036 SNPs  pgid=33
  Loschbour.DG  Luxembourg_Mesolithic.DG  620,881 SNPs  pgid=39136
master_id_bridge: v44.3 I0001 → v66.0 Loschbour (via shared GID Loschbour.DG)
status: present_in_2_of_2_versions; multi_row; individual_id_renamed

Recreate a cohort against a newer release.

aadr-resolve cohort patterson_2022_whga.txt \
    --anno-files v44.3_1240K_public.anno \
    --anno-files v66.0_1240K_public.anno \
    --cohort-version v44.3 \
    -o whga_v66_manifest.tsv

The manifest is a TSV with one row per (individual × library), with per-version genetic_id / group_id / snps_hit_1240k columns plus per-adjacent-pair group_id_change_class_v{old}_to_v{new} columns, ready to feed into downstream relabeling tools like pgen-samplebind.

Output (stdout summary block):

Loaded 2 .anno file(s):
  [v44.3] v44.3_1240K_public.anno: 9,275 rows × 43 cols, class A
  [v66.0] v66.0_1240K_public.anno: 23,250 rows × 49 cols, class E

Cross-version bridge:
  GID-stable MID-rename detection:  9 events
  Manual --mid-bridge entries:      0
  Cross-lab MID collision check:    no collisions detected

Cohort input: patterson_2022_whga.txt (40 individuals)
  Resolved in latest version:  37
  Added after earliest:        1
  Removed before latest:       2

Group ID changes (v44.3 → v66.0):
  convention_restructure_suffix      18
  partial                             1
  substantive_regroup                 2

Wrote whga_v66_manifest.tsv (40 rows × 13 cols)
Sample turnover within cohort: 5.0% — PASS

Done in 1.4s.

Add --quiet to suppress the block. Add --report-json summary.json to also emit a run-level JSON sidecar that loads cheaply via json.load — see docs/REPORT_JSON_SCHEMA.md.

Structured diff between two releases.

aadr-resolve diff v62.0_1240K_public.anno v66.0_1240K_public.anno \
    --tsv > v62_to_v66_changes.tsv

Emits one row per change event: added, removed, genetic_id_renamed, master_id_renamed, group_changed (with a per-class label — convention_restructure_suffix etc.).

For large diffs at AADR scale, stream the per-event TSV alongside a small summary JSON instead of buffering the full event list:

aadr-resolve diff v62.0_1240K_public.anno v66.0_1240K_public.anno \
    -o changes_summary.json \
    --report changes_events.tsv \
    --report-json summary.json

--report PATH streams one row per event (constant memory) and --report-json PATH writes the run-level summary (~few KB, loads cheaply via json.load). The diff stdout summary block routes to stderr when stdout is carrying the JSON payload, so pipes stay clean.

Subcommands

Command	Purpose
lookup	Resolve a single sample across N versions
cohort	Emit a cross-version manifest for a user-supplied cohort
diff	Structured diff between two versions
join	Wide-format pairwise table over the full intersection
schema	Diagnostic: report the detected schema class

aadr-resolve lookup

aadr-resolve lookup INDIVIDUAL_OR_GENETIC_ID \
    --anno-files PATH [--anno-files PATH ...]
    [--json]

Treated as individual_id by default; falls back to genetic_id if no IID matches. The MID-rename bridge is built automatically from the supplied versions and reported under master_id_bridge in the output.

aadr-resolve cohort

aadr-resolve cohort COHORT_FILE \
    --anno-files PATH [--anno-files PATH ...]
    [--cohort-version LABEL]
    -o OUT.tsv [--json]
    [--no-propagate]
    [--collapse-to-individual]
    [--gid-preference AG,DG,SG,HO,TW,BY,AA,EC,WGC,bare]
    [--turnover-warn 0.05] [--turnover-fail 0.30]
    [--cohort-coverage-warn 0.50] [--cohort-coverage-fail 0.25]
    [--report-json PATH]

COHORT_FILE is a TSV: one column for individual_id, optional second column for cohort_label. --cohort-version is auto-detected from the supplied annos when omitted. Default output is row-per-(individual × library); --collapse-to-individual reduces to one row per individual via the --gid-preference suffix priority. --report-json PATH writes a run-level summary sidecar (~few KB) for CI dashboards.

aadr-resolve diff

aadr-resolve diff V_OLD.anno V_NEW.anno
    [--json | --tsv]
    [-o OUT]
    [--include-class CLASS [--include-class CLASS ...]]
    [--all-events]
    [--turnover-warn 0.05] [--turnover-fail 0.30]
    [--substantive-regroup-fail INT]
    [--report PATH] [--report-json PATH]

JSON output is summary-first: per-class counts always included; per-event arrays only for substantive_regroup (always) and any class named via --include-class, or all classes when --all-events is set. --tsv switches to streamed one-row-per-event format.

For large diffs, prefer the streamed sidecars: --report PATH writes per-event TSV with constant memory; --report-json PATH writes the run-level summary. The summary block routes to stderr when stdout is the JSON payload, so aadr-resolve diff a.anno b.anno | jq ... works without breaking the pipe.

aadr-resolve join

aadr-resolve join V_OLD.anno V_NEW.anno
    -o OUT.tsv [--json]
    [--collapse-to-individual]
    [--gid-preference AG,DG,SG,HO,TW,BY,AA,EC,WGC,bare]

Wide-format pairwise table over the full v_old ∪ v_new canonical individual_id set. Same output schema as cohort; useful when you don't have a pre-existing cohort list.

aadr-resolve schema

aadr-resolve schema PATH [--json]

Diagnostic: detects which schema class (A–F) the .anno belongs to, reports the column layout. Useful for debugging "why does this .anno not load."

Shared options

These apply to all subcommands:

Option	Default	Notes
--schema-override CLASS	auto	Force schema class A/B/C/D/E (e.g., renamed .anno)
--version-label LABEL	auto	Force version label (when filename pattern doesn't match)
--mid-bridge FILE	none	Manual master_id-rename TSV layered on auto-detected bridge
--on-mid-collision {error,warn}	error	Cross-lab MID collision policy
--quiet	false	Suppress the stdout summary block (cohort + diff + join write phase)

Library API

The same functionality is available in-process:

from aadr_resolve import (
    AnnoFrame,
    resolve_master_ids,
    resolve_genetic_ids,
)

# Resolve v44.3 Master IDs to v66.0 GeneticIDs
result = resolve_master_ids(
    ["I0001", "Bichon", "Mota"],
    src_version="v44.3",
    dst_version="v66.0",
    anno_paths={
        "v44.3": "v44.3_1240K_public.anno",
        "v66.0": "v66.0_1240K_public.anno",
    },
    mid_bridge="manual_renames.tsv",  # optional override TSV
)
# result = {"I0001": "Loschbour.AG", "Bichon": "Bichon.SG", "Mota": None}

resolve_genetic_ids does the GID → GID inverse:

result = resolve_genetic_ids(
    ["I0001"],
    src_version="v44.3",
    dst_version="v66.0",
    anno_paths={...},
)
# result = {"I0001": ["Loschbour.AG", "Loschbour.DG"]}  # multi-row IID

Both functions also accept anno_frames={label: AnnoFrame, ...} as an alternative to anno_paths={label: path, ...} — useful when you've already loaded the frames once and want to reuse them across calls.

Direct AnnoFrame access for lower-level work:

from aadr_resolve import AnnoFrame

af = AnnoFrame.from_path("v66.0_1240K_public.anno", version_label="v66.0")
af.schema_class       # SchemaClass.E
af.individual_id      # pd.Series of canonical IIDs
af.genetic_id         # pd.Series
af.persistent_genetic_id  # pd.Series of Int64 nullable for class E; None for A-D
af.date_calbp         # pd.Series of Int64 nullable
af.coverage           # pd.Series of Float64 nullable
af.path               # original Path, useful for re-creating anno_paths dicts

Exception hierarchy

All errors derive from aadr_resolve.AadrResolveError. Sibling tools catching aadr-resolve errors can except aadr_resolve.<Class>:

Class	Maps to exit	Trigger
ValidationError	1	Turnover gate, coverage gate, substantive-regroup gate
IOFailure	2	File not found, lock held, malformed TSV
InvariantViolation	3	Schema YAML malformed (rare)
SchemaDetectionError	3	Header signature unknown
MissingNativeFieldError	3	Canonical field requested for a class that lacks it
CollisionDetected	3	Cross-lab MID collision under error policy
UsageError	4	Bad CLI args; cohort file has no matching version

Exit codes

Stable across versions. CI workflows can grep:

• 0 — success
• 1 — soft-validation failure (any of the gates)
• 2 — I/O failure
• 3 — invariant violation (schema, MID collision)
• 4 — usage error (bad CLI args)

Troubleshooting

"unknown .anno schema signature" — your .anno header doesn't match any of the 5 known classes. Either the file is from a newer AADR release (file an issue with the bench-verify diff), or the file has been edited. Workarounds:

• --schema-override A|B|C|D|E|F forces a class without signature check.
• --version-label vN.N forces a version label when the filename doesn't match a known pattern. It sets the version-keying label only — the column layout (for releases that share a class but shift columns, e.g. v50.0) is detected from the header content, so --version-label does not force a layout when the headers indicate a different one.

"cross-lab MID collision" — the GID-stability check found a Master ID that maps to two different individuals in different versions. This indicates either a real data error in AADR or a cross-lab naming collision (rare). Workarounds:

• --on-mid-collision warn continues with a stderr warning and marks affected rows with library_chain_ambiguous status.
• --mid-bridge FILE lets you specify the correct mapping manually.

"sample turnover gate (fail)" — removal rate exceeded the --turnover-fail threshold (default 30%). Indicates either a major AADR cleanup (the v62→v66 bump removed ~17%) or that the wrong files are being compared. Override with --turnover-fail 1.0 to disable.

"cohort coverage gate (fail)" — fewer than 25% of cohort entries resolved in the supplied versions. Usually means the cohort file uses IDs from a version not in the supplied set. Check --cohort-version.

"substantive_regroup gate (fail)" — only fires on diff when --substantive-regroup-fail INT is set and the count of substantive_regroup events exceeds the threshold. Inspect the events via --report PATH or --include-class substantive_regroup before adjusting the threshold.

Pandas ParserError on a v52 / v54 .anno — these versions contain embedded quote characters in some full_date cells. aadr-resolve reads with csv.QUOTE_NONE to side-step pandas's default quote-handling; upgrade if you're on an older version.

Composition with the broader ecosystem

The manifest TSV is the handoff format to downstream relabeling tools. Typical pipeline pairing aadr-resolve's join output with a PLINK2 sample-rename step:

aadr-resolve cohort patterson_2022.txt \
    --anno-files v44.3_1240K_public.anno \
    --anno-files v66.0_1240K_public.anno \
    -o cohort_manifest.tsv
pgen-samplebind merge \
    --relabel-from cohort_manifest.tsv \
    --output merged_v66.pgen \
    v44.3.pgen v66.0.pgen

Cohort manifest column layout

Stable column order across versions:

1. cohort_label, cohort_label_source, individual_id_canonical, library_token
2. Per-version triples in user-supplied order: v{X}_genetic_id, v{X}_group_id, v{X}_snps_hit_1240k
3. Per-adjacent-pair classifier columns: group_id_change_class_v_{old}_to_v_{new} (one per consecutive pair; values: convention_restructure_{suffix,country,order,punct}, partial, substantive_regroup, none, or -- if absent)
4. persistent_genetic_id (only when the latest version is class E and at least one row has a value)
5. status

Missing-cell sentinel is -- for every column (both string fields and nullable-Int64 numerics).

Contributing

• CONTRIBUTING.md covers local development setup, the test layout (default / slow / external / perf markers), lint and type-check invocations, and the release process.
• DEVELOPMENT.md is the architecture tour — module map, data flow, key abstractions, invariants. Start there before filing a non-trivial PR.
• ROADMAP.md tracks deferred work and known scope-cuts.

License

MIT.