Command-line interface
apb-fasta --help
Three commands, one per operation. All take an APB2 result, one or more FASTA files, and a mandatory --output.
verify-peptides
apb-fasta verify-peptides input.h5mu human.fasta contaminants.fasta --output verified.h5mu
Reports per level how many targets the FASTA contains, how many it does not, and the decoys apb2 marked apb_Decoy, which are neither.
merge-annotations
apb-fasta merge-annotations input.h5mu human.fasta contaminants.fasta --output annotated.h5mu
run
apb-fasta run input.h5mu human.fasta contaminants.fasta --output complete.h5mu
Applies both operations in one in-memory pass and reports both coverage summaries.
Options
| Option | Default | Commands |
|---|---|---|
--output |
required | all |
--formats |
uniprotkb refseq |
all |
--protein-group-separator |
; |
all |
--backend |
auto |
verify-peptides, run |
--formats names the protein_fasta header formats to try, in priority order. --backend selects the Prozor Aho-Corasick implementation.
Exit codes
0 on success. 1 on an expected failure — a missing file, a missing level, a protein frame without the required columns, or an output name that already exists. The reason is logged; nothing is written.