[WIP]feat(ref): return NCBI assembly reports via gget ref (#179)#237
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[WIP]feat(ref): return NCBI assembly reports via gget ref (#179)#237Elarwei001 wants to merge 6 commits into
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## dev #237 +/- ##
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+ Coverage 56.70% 57.31% +0.61%
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Add an `assembly_report` mode to `gget ref` (Python API and CLI). When enabled, the positional argument is interpreted as an NCBI assembly accession (e.g. GCF_000001405.40) and the NCBI assembly report is fetched and parsed, mapping sequence/chromosome names across the Ensembl/short, GenBank, RefSeq and UCSC naming conventions. - New `gget.assembly_report()` helper and `ref(..., assembly_report=True)`. - CLI: `gget ref <accession> --assembly_report [--csv]`. - Returns a pandas DataFrame by default, list of dicts / JSON with json=True. - Tests + fixtures (live NCBI, small SARS-CoV-2 assembly) and docs. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Add a network-free TestAssemblyReportOffline class that mocks requests to cover assembly_report (accession validation, parent-dir and report HTTP errors, no-folder/missing-header errors, parsing, verbose, and json/save/CSV branches) and the ref(assembly_report=True) delegation. All PR-added lines are now covered except the json_package.dump rename deep in the Ensembl network save path (un-coverable network-free). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Bilingual (ZH/EN) analysis of scverse/gget#237 (adds assembly_report to gget ref: interpret the positional arg as an NCBI assembly accession, return the cross-naming map chr1<->1<->CM000663.2<->NC_000001.11). Covers platform fit, the --csv-inverted-vs-gget-norm UX wart, and the de-facto live fixture test. Updated README index + index.html card. Analysis by subagent. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…on-less accession (scverse#179) Addresses review findings on the assembly_report feature: - --csv now follows gget's convention: it is store_false (default JSON on the CLI, --csv converts to CSV), so a flag named --csv gives CSV like every other module, instead of the previous inverted behaviour (--csv -> JSON). - Directory match uses `startswith(accession + "_")` so e.g. 'GCF_000001405.4' no longer prefix-matches the folder for 'GCF_000001405.40'. - The accession version suffix is now optional; when omitted (e.g. 'GCF_000001405') the latest available version is resolved. Saved files and logs carry the resolved version. - Move the network-touching fixture out of test_ref.json into an explicit TestAssemblyReportLive (skip-on-network / transient; anchored to the frozen SARS-CoV-2 report but asserting only stable identity columns). Add offline tests for the version-prefix guard and the version-less latest resolution. - Fix a pre-existing mypy error on df.to_dict(orient="records") via cast. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…cverse#179) assembly_report previously required an NCBI assembly accession. Add an explicit `taxon=True` option (CLI `--taxon`/`-tx`) that interprets the input as an organism/taxon name (e.g. "homo sapiens") and resolves it to that taxon's NCBI reference assembly accession before fetching the report, using the datasets CLI already bundled with gget. - Resolution is opt-in: accession callers are unaffected and make no extra call. gget_virus (for the datasets binary) is imported lazily, only in taxon mode. - Default resolves to the reference assembly; to fetch a specific non-reference assembly, pass its accession directly. - Tests: offline (taxon path wiring, resolver parsing, not-found -> ValueError, datasets failure -> RuntimeError) and a live test resolving "homo sapiens". - Docs: --taxon flag + example (en); changelog note. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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…rse#179) Complements --taxon (which resolves to the reference assembly): --list_assemblies (Python: list_assemblies=True) interprets the input as an organism/taxon name and returns a table of all NCBI assemblies for that taxon (accession, assembly_name, refseq_category, assembly_level, organism), with reference/representative first, so a user can discover and then fetch a specific non-reference assembly by accession. Uses the bundled datasets CLI (imported lazily). Tests: offline (parse/order, empty -> ValueError, delegation) and a live test listing the human assemblies. Docs: --list_assemblies flag + example; changelog note. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Hi @lauraluebbert — gget ref --assembly_report (resolves #179) fetches an NCBI assembly report to translate sequence/chromosome names across Ensembl/GenBank/RefSeq/UCSC. Key points:
would appreciate a review when you have a moment. Thanks |
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Resolves #179
What this adds
gget ref --assembly_report(Python:assembly_report=True) fetches the NCBI assembly report for an assembly and returns it as apandasDataFrame (or list of dicts withjson=True). The report maps each sequence/chromosome name across the Ensembl/short, GenBank, RefSeq, and UCSC conventions (e.g.1↔CM000663.2↔NC_000001.11↔chr1), which is handy for translating chromosome names between databases. A standalonegget.assembly_report()is also exposed.GCF_000001405(no version) and the latest version is resolved automatically.--taxon(Python:taxon=True) interprets the input as an organism name (e.g."homo sapiens") and resolves it to that taxon's NCBI reference assembly via the bundleddatasetsCLI, so you don't need to know the accession.--list_assemblies(Python:list_assemblies=True) lists all NCBI assemblies for an organism name (accession, name, category, level; reference/representative first), so you can pick a specific non-reference assembly to fetch.--csvfor CSV.Name resolution (
--taxon/--list_assemblies) is opt-in and imported lazily, so accession callers are unaffected and make no extra call.How it works
Builds the NCBI FTP path by sharding the accession digits (
GCA/981/441/385/…), lists the parent directory to find the exact assembly folder (matched precisely so.4can't collide with.40), then parses the tab-delimited*_assembly_report.txt. Organism-name modes shell out to the bundleddatasets summary genome taxonCLI.Testing
tests/test_ref.py): report parsing, json/save paths, the five error branches, version-prefix guard, version-less latest resolution, taxon resolution and assembly listing (parse / order / not-found / datasets-failure), and theref()delegation.TestAssemblyReportLive, skip-on-network/transient): SARS-CoV-2 report anchored on stable identity columns,--taxon "homo sapiens"resolving to the human reference, and--list_assemblieslisting the human assemblies.