Metadata-Version: 2.4
Name: sar11-genome-atlas-tools
Version: 0.1.1
Summary: SGAmapper and SGAclassifier for the SAR11 Genome Atlas
Author: SAR11 Genome Atlas team
License: MIT
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: biopython>=1.80
Requires-Dist: pandas>=2.0
Requires-Dist: pyyaml>=6.0
Requires-Dist: rich>=13.7
Dynamic: license-file

# SGAtoolkit

SGAtoolkit is a conda-distributed command-line toolkit for the SAR11 Genome
Atlas. It combines gene prediction, SAR11 Genome Atlas OG mapping, and
conservative SAR11 phylogenetic classification.

The implementation is intentionally separated from the existing SAR11 Genome Atlas web
assets. The current directory contains the package layout, bundled compact
reference data, and the conda recipe location. The executable workflows are
`sga-mapper`, `sga-classify`, and `sga-run`; `sga-map` remains a compatibility
alias.

```bash
sga-mapper proteins.faa --output-dir results/mapper
sga-classify proteins.faa --onlyalign --output-dir results/alignment
sga-classify genome.fna --output-dir results/classifier
sga-run genome.fna --output-dir results/sample
sga-run fna_dir/ --output-dir results/batch --threads 8
```

The main commands also accept directories containing homogeneous FAA or FNA
inputs as appropriate. `sga-mapper` accepts FAA, full `sga-classify` and
`sga-run` accept FNA, and `sga-classify --onlyalign` accepts either format.
Batch mode shares HMM searches, marker-wise MAFFT, and phylogenetic placement
across samples instead of looping over complete single-genome runs. If a
directory mixes FAA and FNA files, SGAtoolkit prints a warning and processes
only matching files; a directory with no matching files is an error.

On the first run, missing runtime databases are downloaded to
`~/.cache/sga-toolkit/` and reused later. Set `SGA_CACHE_DIR` to use a
different writable cache. The three runtime archives are published in the
[GAtools datasets Zenodo record](https://zenodo.org/records/21726922):
`SAR11_Orthogroups_4577.hmm.tar.gz`, `SAR11_165_marker_hmms.tar.gz`, and
`fna_files.tar.gz`.

See [`docs/SGAtoolkit_design.md`](docs/SGAtoolkit_design.md) for the workflow,
data policy, output schema, and release plan.
