PeptideIndexing

class pyopenms.PeptideIndexing

Bases: object

Cython implementation of _PeptideIndexing

Original C++ documentation is available here

– Inherits from [‘DefaultParamHandler’]

Refreshes the protein references for all peptide hits in a vector of PeptideIdentifications and adds target/decoy information

All peptide and protein hits are annotated with target/decoy information, using the meta value “target_decoy”. For proteins the possible values are “target” and “decoy”, depending on whether the protein accession contains the decoy pattern (parameter decoy_string) as a suffix or prefix, respectively (see parameter prefix). For peptides, the possible values are “target”, “decoy” and “target+decoy”, depending on whether the peptide sequence is found only in target proteins, only in decoy proteins, or in both. The target/decoy information is crucial for the @ref TOPP_FalseDiscoveryRate tool. (For FDR calculations, “target+decoy” peptide hits count as target hits.)

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: PeptideIndexing) → None

Methods

__init__
getDecoyString(self)
getDefaults(self)	Returns the default parameters
getName(self)	Returns the name
getParameters(self)	Returns the parameters
getSubsections(self)
isPrefix(self)
run(self, proteins, prot_ids, pep_ids)
setName(self, in_0)	Sets the name
setParameters(self, param)	Sets the parameters

PeptideIndexing_ExitCodes

alias of __PeptideIndexing_ExitCodes

getDecoyString(self) → bytes | str | String

getDefaults(self) → Param

Returns the default parameters

getName(self) → bytes | str | String

Returns the name

getParameters(self) → Param

Returns the parameters

getSubsections(self) → List[bytes]

isPrefix(self) → bool

run(self, proteins: List[FASTAEntry], prot_ids: List[ProteinIdentification], pep_ids: PeptideIdentificationList) → int

setName(self, in_0: bytes | str | String) → None

Sets the name

setParameters(self, param: Param) → None

Sets the parameters