Python API
Annotation lifecycle
Public in-memory FASTA annotation API.
FastaAnnotationParameters
dataclass
Configuration shared by peptide validation and protein annotation.
__post_init__()
Reject a separator that cannot define protein-group members.
FastaAnnotationReports
dataclass
Persistable aggregate evidence from one annotation application.
FastaAnnotationResult
dataclass
A replacement APB2 result and its FASTA reports.
FastaAnnotator
Bind one protein database and its FASTA annotation behavior.
proteins
property
The bound protein table, one row per FASTA entry in file order.
__init__(proteins, parameters=DEFAULT_FASTA_ANNOTATION_PARAMETERS)
Validate and bind a reusable protein database and configuration.
annotate(parsed)
Verify peptides and then merge protein annotations in memory.
merge_annotations(parsed)
Merge FASTA annotations for every reported protein-group member.
read(fasta, formats=('uniprotkb', 'refseq'), parameters=DEFAULT_FASTA_ANNOTATION_PARAMETERS)
classmethod
Read FASTA files, or the protein-fasta database Parquet written from them.
verify_peptides(parsed)
Verify every canonical stripped peptide against the protein sequences.
add_peptide_properties(parsed)
Attach sequence-derived properties to every peptide-derived level.
Writes a feature-aligned varm["peptide_properties"] computed by
protein_fasta.peptide_frame.peptide_property_frame from each level's ProForma_peptide.
No protein database is needed. A feature without a sequence, or with a residue outside the 20
standard amino acids, has null properties.
Raises:
| Type | Description |
|---|---|
FastaAnnotationError
|
If the result has no peptide-derived level, already contains the output, or already records the operation. |
ValueError
|
If a sequence is not stripped upper-case letters. |
Configuration
User-selected FASTA annotation behavior.
FastaAnnotationParameters
dataclass
Configuration shared by peptide validation and protein annotation.
__post_init__()
Reject a separator that cannot define protein-group members.
Errors
Expected APB FASTA annotation failures.
FastaAnnotationError
Bases: ValueError
The supplied APB2 result or protein frame cannot be annotated safely.
Reports
Immutable calculation values returned to the APB2 integration boundary.
FastaAnnotationReports
dataclass
Persistable aggregate evidence from one annotation application.
PeptideCoverage
dataclass
Aggregate FASTA coverage for one APB2 feature level.
decoy_feature_count
instance-attribute
Rows apb2 marked apb_Decoy; a decoy is neither matched nor unmatched.
il_only_matched_feature_count
instance-attribute
Targets in matched_feature_count whose peptide matches only as another I/L spelling.
matched_feature_count
instance-attribute
Targets, rows apb2 did not mark apb_Decoy, whose peptide the FASTA contains.
unmatched_feature_count
instance-attribute
Targets whose peptide the FASTA does not contain.
PeptideLevelMatch
dataclass
Feature-aligned peptide facts and their aggregate coverage.
ProteinGroupCoverage
dataclass
Aggregate FASTA coverage for reported protein-group members.
ProteinGroupMatch
dataclass
Lossless member expansion, group summaries, and source relation.