PEFFEntry#

class pyopenms.PEFFEntry(*args, **kwargs)#

Bases: object

Represents a single entry in a PEFF file with all annotations. Each entry corresponds to one description line and sequence. The description line format is: >Prefix:DbUniqueId \key=value … Attributes: prefix: Database prefix from description line identifier: Protein identifier (Prefix:DbUniqueId) sequence: Amino acid sequence protein_names: List of protein names gene_name: Gene name ncbi_tax_id: NCBI taxonomy ID taxonomy_name: Taxonomy name sequence_length: Sequence length modifications: List of modifications simple_variants: List of simple variants complex_variants: List of complex variants processed_regions: List of processed regions proteoforms: List of proteoforms in ProForma notation

__init__(self) → None#
__init__(self, arg: pyopenms._pyopenms_format.PEFFEntry, /) → None

Attributes

`alt_accessions`	(self) -> list[str]
`complex_variants`	(self) -> list[OpenMS::PEFFVariantComplex]
`custom_annotations`	(self) -> dict[str, str]
`db_unique_id`	(self) -> str
`digestWithVariants`	Digest with variants.
`disulfide_bonds`	(self) -> list[pyopenms._pyopenms_format.PEFFDisulfideBond]
`entry_id`	(self) -> str
`entry_version`	(self) -> str
`fromFASTAEntry`
`gene_name`	(self) -> str
`generatePeptides`	Generate peptides with PEFF annotations.
`getModifiedSequence`	Get an AASequence with all annotated modifications applied.
`getProcessedSequence`	Get processed sequence (e.g., mature protein without signal peptide).
`getSequence`	Get the base AASequence for this entry (unmodified sequence)
`getVariantSequences`	Get all variant sequences (each variant applied individually).
`identifier`	(self) -> str
`modifications`	(self) -> list[OpenMS::PEFFModification]
`ncbi_tax_id`	(self) -> int
`prefix`	(self) -> str
`processed_regions`	(self) -> list[OpenMS::PEFFProcessedRegion]
`protein_existence`	(self) -> int
`protein_names`	(self) -> list[str]
`proteoforms`	(self) -> list[str]
`sequence`	(self) -> str
`sequence_length`	(self) -> int
`sequence_version`	(self) -> str
`simple_variants`	(self) -> list[OpenMS::PEFFVariantSimple]
`taxonomy_name`	(self) -> str
`toFASTAEntry`

property alt_accessions#: (self) -> list[str]

property complex_variants#: (self) -> list[OpenMS::PEFFVariantComplex]

property custom_annotations#: (self) -> dict[str, str]

property db_unique_id#: (self) -> str

digestWithVariants#: Digest with variants. Returns (descriptions, sequences)

property disulfide_bonds#: (self) -> list[pyopenms._pyopenms_format.PEFFDisulfideBond]

property entry_id#: (self) -> str

property entry_version#: (self) -> str

fromFASTAEntry = <nanobind.nb_func object>#

property gene_name#: (self) -> str

generatePeptides#: Generate peptides with PEFF annotations. Returns (descriptions, sequences)

getModifiedSequence#: Get an AASequence with all annotated modifications applied. Modifications with unknown positions (position == 0) or that cannot be resolved are skipped.

getProcessedSequence#: Get processed sequence (e.g., mature protein without signal peptide). :param region_accession: PEFF CV accession of the region type (e.g., “PEFF:0001021” for signal peptide) :return: Processed AASequence, or an empty AASequence if no region has this accession

getSequence#: Get the base AASequence for this entry (unmodified sequence)

getVariantSequences#: Get all variant sequences (each variant applied individually). :param include_complex: If True, also include complex variants; otherwise only simple variants :return: Tuple (descriptions, sequences) of variant descriptions and AASequences

property identifier#: (self) -> str

property modifications#: (self) -> list[OpenMS::PEFFModification]

property ncbi_tax_id#: (self) -> int

property prefix#: (self) -> str

property processed_regions#: (self) -> list[OpenMS::PEFFProcessedRegion]

property protein_existence#: (self) -> int

property protein_names#: (self) -> list[str]

property proteoforms#: (self) -> list[str]

property sequence#: (self) -> str

property sequence_length#: (self) -> int

property sequence_version#: (self) -> str

property simple_variants#: (self) -> list[OpenMS::PEFFVariantSimple]

property taxonomy_name#: (self) -> str

toFASTAEntry#