gapit 0.2.2__py3-none-any.whl

gapit-0.2.2.dist-info/METADATA

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+Metadata-Version: 2.5
+Name: gapit
+Version: 0.2.2
+Summary: Mass screening of contigs for antimicrobial resistance and virulence genes — agent-first Python reimplementation of abricate
+Project-URL: Homepage, https://github.com/indexofire/gapit
+Project-URL: Documentation, https://indexofire.github.io/gapit/
+Project-URL: Changelog, https://github.com/indexofire/gapit/blob/main/CHANGELOG.md
+Project-URL: Source, https://github.com/indexofire/gapit
+Project-URL: Issues, https://github.com/indexofire/gapit/issues
+Author-email: indexofire <indexofire@gmail.com>
+License-Expression: MIT
+License-File: LICENSE
+Keywords: AMR,bioinformatics,blast,genomics,virulence
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Requires-Dist: pydantic>=2.7
+Requires-Dist: rich>=13
+Requires-Dist: typer>=0.12
+Description-Content-Type: text/markdown
+
+# gapit
+
+Mass screening of contigs and reads for antimicrobial resistance and virulence genes. An
+agent-first Python reimplementation of [abricate](https://github.com/tseemann/abricate):
+byte-compatible TSV plus first-class JSON and Markdown.
+
+## Why gapit
+
+- **Drop-in abricate replacement.** Same BLAST pipeline, same hit rules, abricate-format
+  TSV on stdout. Parity with abricate 1.4.0 is a release gate, checked by diffing gene
+  calls against real abricate (`pixi run -e parity parity`).
+- **Machine-readable by design.** Versioned output schemas (`gapit.report/1`,
+  `gapit.reads/1`, `gapit.summary/1`), self-describing via `gapit schema`, typed JSON error
+  envelopes on stderr, documented exit codes. An agent can discover the whole contract
+  without reading docs.
+- **Reads, not just contigs.** `gapit screen --r1/--r2` screens FASTQ through minimap2, and
+  `--r1` accepts assembly FASTA directly (content-detected, `map-ont` forced) for a fast
+  presence survey. abricate cannot screen raw reads.
+
+## Install
+
+[pixi](https://pixi.sh) manages the environment, including the external binaries
+(BLAST+, minimap2):
+
+```bash
+git clone https://github.com/indexofire/gapit.git
+cd gapit
+pixi install
+pixi run gapit --version
+```
+
+The package supports Python 3.11+; the dev environment pins 3.14.
+
+## Quick start
+
+```bash
+# Screen contigs (abricate-compatible TSV on stdout, --db defaults to ncbi)
+gapit screen contigs.fa --db ncbi
+
+# Agent- and human-readable outputs
+gapit screen contigs.fa --db ncbi --format json
+gapit screen contigs.fa --format md
+
+# Screen FASTQ reads; --read-type picks the minimap2 preset
+gapit screen --r1 sample_R1.fastq.gz --r2 sample_R2.fastq.gz --read-type sr --db card
+gapit screen --r1 ont_reads.fastq.gz --read-type map-ont --format json
+
+# Summarize report tables into a gene presence/absence matrix
+gapit summary *.tsv
+
+# Databases: card + vfdb install offline from bundled snapshots, others fetch on demand
+gapit db fetch
+gapit db fetch ncbi
+gapit db list
+gapit db outdated                # flag stale databases and newer bundled snapshots
+gapit db search "tet(M)"         # look up genes across every installed database
+gapit db build mydb my_genes.fa --tsv my_meta.tsv   # custom db from any FASTA
+
+# Introspection
+gapit list              # installed databases (abricate --list compatible)
+gapit schema report     # JSON Schema of gapit.report/1
+```
+
+Contig screening follows abricate defaults (`--minid 80`, `--mincov 80`). Reads-mode
+presence defaults to 90% alignment breadth (`--min-breadth 90`).
+
+## Databases
+
+A database is a directory under the datadir, resolved from `$GAPIT_DATADIR`, then
+`~/.local/share/gapit/db` (override per call with `--datadir`). Twelve providers exist;
+`card` and `vfdb` ship inside the wheel and install with zero network, the rest download
+from upstream when fetched.
+
+| Name | Content | dbtype |
+|---|---|---|
+| `ncbi` | NCBI AMRFinderPlus curated AMR (default db) | nucl |
+| `card` | CARD protein homolog resistance models | nucl |
+| `resfinder` | CGE ResFinder acquired resistance genes | nucl |
+| `argannot` | ARG-ANNOT acquired resistance genes | nucl |
+| `plasmidfinder` | CGE PlasmidFinder replicons | nucl |
+| `megares` | MEGARes antimicrobial resistance genes | nucl |
+| `ecoh` | E. coli O and H antigens (srst2 EcOH) | nucl |
+| `vfdb` | VFDB virulence factors (set A, nucleotide) | nucl |
+| `ecoli_vf` | E. coli virulence factors | nucl |
+| `bacmet2` | BacMet2 biocide/resistance genes (protein) | prot |
+| `victors` | Victors virulence factors | nucl |
+| `upec_expec_vf` | UPEC/ExPEC virulence genes | nucl |
+
+gapit also reads datadirs built by abricate itself (legacy `~~~` headers). The reverse
+does not hold: gapit-native databases use the `gapit/v1` header format (see SPEC.md §11),
+which abricate cannot read. Protein databases such as `bacmet2` screen through blastx.
+
+## Output contract
+
+- **stdout purity.** Data on stdout, diagnostics on stderr, always. `--quiet` silences
+  stderr only.
+- **Deterministic.** Stable sort orders, fixed tool parameters, no wall-clock timestamps
+  inside data payloads.
+- **Errors** print a JSON envelope to stderr and exit nonzero:
+
+```text
+{"schema": "gapit.error/1", "code": "...", "message": "...", "context": {...}}
+```
+
+| Exit code | Meaning |
+|---|---|
+| 0 | success |
+| 1 | unexpected error |
+| 2 | usage error |
+| 3 | missing dependency |
+| 4 | database error |
+| 5 | input error |
+
+## MCP server
+
+gapit ships an MCP (Model Context Protocol) stdio server so agent runtimes can
+screen assemblies without parsing CLI output: `gapit mcp` or the `gapit-mcp`
+console script speaks newline-delimited JSON-RPC 2.0 on stdin/stdout (no extra
+dependencies — the protocol is hand-rolled). It exposes nine tools:
+`screen` (gapit.report/1 by default; `aligner minimap2` for a fast assembly
+survey), `screen_reads` (FASTQ via minimap2, gapit.reads/1), `summary`
+(gapit.summary/1), `schema`, `db_list`, plus the database tools `db_fetch`,
+`db_build`, `db_search`, and `db_outdated` so an agent can self-provision
+and inspect databases mid-session.
+Tool failures return `isError: true` with the `gapit.error/1` envelope as text.
+Register it with an MCP client:
+
+```json
+{"mcpServers": {"gapit": {"command": "gapit-mcp"}}}
+```
+
+## Development
+
+| Task | Runs |
+|---|---|
+| `pixi run lint` | ruff check |
+| `pixi run fmt` | ruff format |
+| `pixi run typecheck` | basedpyright (strict) |
+| `pixi run test` | pytest, 374 offline tests |
+| `pixi run -e parity parity` | byte-diff screening vs real abricate |
+| `pixi run -e parity summary-parity` | byte-diff summary vs real abricate |
+
+User documentation lives in [`docs/index.md`](docs/index.md), rendered at
+<https://indexofire.github.io/gapit/>.
+
+`SPEC.md` is the parity contract, `PLAN.md` the roadmap, `AGENTS.md` the contributor
+guide, `CHANGELOG.md` the change history.
+
+## License
+
+gapit is MIT-licensed. It is a behavioral reimplementation of abricate (GPL-2.0) and
+copies no Perl code; abricate itself remains GPL-2.0. Bundled database content retains
+its original upstream licenses (SPEC.md §9).

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gapit-0.2.2.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: hatchling 1.32.4
+Root-Is-Purelib: true
+Tag: py3-none-any

gapit-0.2.2.dist-info/entry_points.txt

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+[console_scripts]
+gapit = gapit.cli:app
+gapit-mcp = gapit.mcp:main

gapit-0.2.2.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2026 indexofire
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.