ProteinIdentification#
- class pyopenms.ProteinIdentification#
Bases:
object
Cython implementation of _ProteinIdentification
- Original C++ documentation is available here
– Inherits from [‘MetaInfoInterface’]
- __init__()#
Overload:
- __init__(self) None
Overload:
- __init__(self, in_0: ProteinIdentification) None
Methods
Overload:
Overload:
assignRanks
(self)Sorts the protein hits by score and assigns ranks (best score has rank 1)
clearMetaInfo
(self)Removes all meta values
computeCoverage
(self, pep_ids)Compute the coverage (in percent) of all ProteinHits given PeptideHits
getDateTime
(self)Returns the date of the protein identification run
getHits
(self)Returns the protein hits
getIdentifier
(self)Returns the identifier
Returns the indistinguishable proteins
getKeys
(self, keys)Fills the given vector with a list of all keys for which a value is set
getMetaValue
(self, in_0)Returns the value corresponding to a string, or
Overload:
getProteinGroups
(self)Returns the protein groups
getScoreType
(self)Returns the protein score type
getSearchEngine
(self)Returns the type of search engine used
getSearchEngineVersion
(self)Returns the search engine version
getSearchParameters
(self)Returns the search parameters
getSignificanceThreshold
(self)Returns the protein significance threshold value
insertHit
(self, input)Appends a protein hit
insertIndistinguishableProteins
(self, group)Appends new indistinguishable proteins
insertProteinGroup
(self, group)Appends a new protein group
isHigherScoreBetter
(self)Returns true if a higher score represents a better score
isMetaEmpty
(self)Returns if the MetaInfo is empty
metaRegistry
(self)Returns a reference to the MetaInfoRegistry
metaValueExists
(self, in_0)Returns whether an entry with the given name exists
removeMetaValue
(self, in_0)Removes the DataValue corresponding to name if it exists
setDateTime
(self, date)Sets the date of the protein identification run
setHigherScoreBetter
(self, higher_is_better)Sets the orientation of the score (is higher better?)
setHits
(self, hits)Sets the protein hits
setIdentifier
(self, id_)Sets the identifier
setMetaValue
(self, in_0, in_1)Sets the DataValue corresponding to a name
Overload:
setScoreType
(self, type)Sets the protein score type
setSearchEngine
(self, search_engine)Sets the search engine type
setSearchEngineVersion
(self, ...)Sets the search engine version
setSearchParameters
(self, search_parameters)Sets the search parameters
setSignificanceThreshold
(self, value)Sets the protein significance threshold value
sort
(self)Sorts the protein hits according to their score
- PeakMassType#
alias of
__PeakMassType
- addPrimaryMSRunPath()#
Overload:
- addPrimaryMSRunPath(self, s: List[bytes]) None
Overload:
- addPrimaryMSRunPath(self, s: List[bytes], raw: bool) None
- assignRanks(self) None #
Sorts the protein hits by score and assigns ranks (best score has rank 1)
- clearMetaInfo(self) None #
Removes all meta values
- computeCoverage(self, pep_ids: List[PeptideIdentification]) None #
Compute the coverage (in percent) of all ProteinHits given PeptideHits
- getHits(self) List[ProteinHit] #
Returns the protein hits
- getIndistinguishableProteins(self) List[ProteinGroup] #
Returns the indistinguishable proteins
- getKeys(self, keys: List[bytes]) None #
Fills the given vector with a list of all keys for which a value is set
- getMetaValue(self, in_0: bytes | str | String) int | float | bytes | str | List[int] | List[float] | List[bytes] #
Returns the value corresponding to a string, or
- getPrimaryMSRunPath()#
Overload:
- getPrimaryMSRunPath(self, output: List[bytes]) None
Overload:
- getPrimaryMSRunPath(self, output: List[bytes], raw: bool) None
- getProteinGroups(self) List[ProteinGroup] #
Returns the protein groups
- getSearchParameters(self) SearchParameters #
Returns the search parameters
- getSignificanceThreshold(self) float #
Returns the protein significance threshold value
- insertHit(self, input: ProteinHit) None #
Appends a protein hit
- insertIndistinguishableProteins(self, group: ProteinGroup) None #
Appends new indistinguishable proteins
- insertProteinGroup(self, group: ProteinGroup) None #
Appends a new protein group
- isHigherScoreBetter(self) bool #
Returns true if a higher score represents a better score
- isMetaEmpty(self) bool #
Returns if the MetaInfo is empty
- metaRegistry(self) MetaInfoRegistry #
Returns a reference to the MetaInfoRegistry
- metaValueExists(self, in_0: bytes | str | String) bool #
Returns whether an entry with the given name exists
- removeMetaValue(self, in_0: bytes | str | String) None #
Removes the DataValue corresponding to name if it exists
- setHigherScoreBetter(self, higher_is_better: bool) None #
Sets the orientation of the score (is higher better?)
- setHits(self, hits: List[ProteinHit]) None #
Sets the protein hits
- setMetaValue(self, in_0: bytes | str | String, in_1: int | float | bytes | str | List[int] | List[float] | List[bytes]) None #
Sets the DataValue corresponding to a name
- setPrimaryMSRunPath()#
Overload:
- setPrimaryMSRunPath(self, s: List[bytes]) None
Set the file paths to the primary MS runs (usually the mzML files obtained after data conversion from raw files)
- Parameters:
raw – Store paths to the raw files (or equivalent) rather than mzMLs
Overload:
- setPrimaryMSRunPath(self, s: List[bytes], raw: bool) None
- setSearchEngineVersion(self, search_engine_version: bytes | str | String) None #
Sets the search engine version
- setSearchParameters(self, search_parameters: SearchParameters) None #
Sets the search parameters
- setSignificanceThreshold(self, value: float) None #
Sets the protein significance threshold value
- sort(self) None #
Sorts the protein hits according to their score