APB FASTA
FASTA verification and protein annotation for APB2 results.
apb-fasta takes one APB2 result and FASTA files, or their parsed protein database, and returns a replacement result. It never opens result files itself, and it never receives raw AnnData or MuData objects — protein_fasta owns FASTA reading and header interpretation, Prozor owns peptide matching, and APB2 owns result persistence.
Two independent operations
| Operation | What it does |
|---|---|
verify_peptides |
Confirms every modification-stripped peptide sequence occurs in the supplied FASTA database |
merge_annotations |
Merges FASTA annotations for every reported protein-group member, without collapsing the group to its leading accession |
Each operation is independently callable and independently persistable. FastaAnnotator.annotate() applies both in memory without an intermediate file; the CLI retains the concise run command.
Protein inference with Prozor is the planned third operation. It will remain explicit and opt-in.
Install
Users: pip install apb-fasta. Contributors: uv sync resolves APB2, protein_fasta and Prozor from sibling folders, so clone all four side by side:
git clone https://github.com/anndata-omics-bridge/apb2.git
git clone https://github.com/anndata-omics-bridge/protein-fasta.git protein_fasta
git clone https://github.com/anndata-omics-bridge/prozor.git
git clone https://github.com/anndata-omics-bridge/apb-fasta.git
cd apb-fasta
uv sync --group dev --group docs
Next
- Verify peptides and annotate proteins — the end-to-end guide
- Result layout — what the operations write into the result
- Command-line interface and Python API
- Architecture — module boundaries and the import direction