apb-fasta

FASTA verification and protein annotation for APB2 results.

Online documentation or its source index.

The first release exposes two independent operations:

• verify that APB2's modification-stripped peptide sequences occur in the supplied FASTA database;
• merge FASTA annotations for every reported protein-group member without collapsing the group to its leading accession.

Protein inference with Prozor is the planned third operation. It will remain explicit and opt-in.

Installation

APB FASTA requires Python 3.13 or later.

pip install apb-fasta

Python API

Read the FASTA files once and load the APB2 result:

from pathlib import Path

from apb2.api import read_parsed_levels, write_parsed_levels
from apb_fasta.api import FastaAnnotator

annotator = FastaAnnotator.read((Path("human.fasta"), Path("contaminants.fasta")))
parsed = read_parsed_levels(Path("input.h5mu"))

Verify peptides only:

verified = annotator.verify_peptides(parsed)
print(verified.reports.peptide_levels)
write_parsed_levels(verified.parsed, Path("verified.h5mu"))

Merge protein annotations only:

annotated = annotator.merge_annotations(parsed)
print(annotated.reports.protein_groups)
write_parsed_levels(annotated.parsed, Path("annotated.h5mu"))

Apply both operations in memory:

complete = annotator.annotate(parsed)
write_parsed_levels(complete.parsed, Path("complete.h5mu"))

The operations can also be chained explicitly without an intermediate file:

verified = annotator.verify_peptides(parsed)
complete = annotator.merge_annotations(verified.parsed)

The annotator validates and binds the reusable protein frame once. Every method accepts one canonical ParsedLevels value and returns an immutable FastaAnnotationResult containing its replacement plus typed operation reports. apb_fasta neither opens result files nor receives raw AnnData or MuData objects.

CLI

Verify peptides only:

apb-fasta verify-peptides input.h5mu human.fasta contaminants.fasta --output verified.h5mu

Merge protein annotations only:

apb-fasta merge-annotations input.h5mu human.fasta contaminants.fasta --output annotated.h5mu

Apply both operations together:

apb-fasta run input.h5mu human.fasta contaminants.fasta --output complete.h5mu

Peptide verification adds feature-aligned varm["fasta_validation"] tables. Protein annotation adds protein-aligned varm["fasta"], the lossless fasta_protein_group_members annotation table, and its directed relation to the protein axis.