DigestionEnzymeRNA#

class pyopenms.DigestionEnzymeRNA#

Bases: object

Cython implementation of _DigestionEnzymeRNA

Original C++ documentation is available here: – Inherits from [‘DigestionEnzyme’]

Representation of a digestion enzyme for RNA (RNase)

The cutting sites of these enzymes are defined using two different mechanisms: First, a single regular expression that is applied to strings of unmodified RNA sequence and defines cutting sites via zero-length matches (using lookahead/lookbehind assertions). This is the same mechanism that is used for proteases (see ProteaseDigestion). However, due to the complex notation involved, this approach is not practical for modification-aware digestion. Thus, the second mechanism uses two regular expressions (“cuts after”/”cuts before”), which are applied to the short codes (e.g. “m6A”) of sequential ribonucleotides. If both expressions match, then there is a cutting site between the two ribonucleotides.

There is support for terminal (5’/3’) modifications that may be generated on fragments as a result of RNase cleavage. A typical example is 3’-phosphate, resulting from cleavage of the phosphate backbone.

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: DigestionEnzymeRNA) → None

Methods

`__init__`	Overload:
`addSynonym`(self, synonym)	Adds a synonym
`getCutsAfterRegEx`(self)	Returns the "cuts after ..." regular expression
`getCutsBeforeRegEx`(self)	Returns the "cuts before ..." regular expression
`getFivePrimeGain`(self)	Returns the 5' gain
`getName`(self)	Returns the name of the enzyme
`getRegEx`(self)	Returns the cleavage regex
`getRegExDescription`(self)	Returns the regex description
`getSynonyms`(self)	Returns the synonyms
`getThreePrimeGain`(self)	Returns the 3' gain
`setCutsAfterRegEx`(self, value)	Sets the "cuts after ..." regular expression
`setCutsBeforeRegEx`(self, value)	Sets the "cuts before ..." regular expression
`setFivePrimeGain`(self, value)	Sets the 5' gain
`setName`(self, name)	Sets the name of the enzyme
`setRegEx`(self, cleavage_regex)	Sets the cleavage regex
`setRegExDescription`(self, value)	Sets the regex description
`setSynonyms`(self, synonyms)	Sets the synonyms
`setThreePrimeGain`(self, value)	Sets the 3' gain
`setValueFromFile`(self, key, value)	Sets the value of a member variable based on an entry from an input file

addSynonym(self, synonym: bytes | str | String) → None#: Adds a synonym

getCutsAfterRegEx(self) → bytes | str | String#: Returns the “cuts after …” regular expression

getCutsBeforeRegEx(self) → bytes | str | String#: Returns the “cuts before …” regular expression

getFivePrimeGain(self) → bytes | str | String#: Returns the 5’ gain

getName(self) → bytes | str | String#: Returns the name of the enzyme

getRegEx(self) → bytes | str | String#: Returns the cleavage regex

getRegExDescription(self) → bytes | str | String#: Returns the regex description

getSynonyms(self) → Set[bytes]#: Returns the synonyms

getThreePrimeGain(self) → bytes | str | String#: Returns the 3’ gain

setCutsAfterRegEx(self, value: bytes | str | String) → None#: Sets the “cuts after …” regular expression

setCutsBeforeRegEx(self, value: bytes | str | String) → None#: Sets the “cuts before …” regular expression

setFivePrimeGain(self, value: bytes | str | String) → None#: Sets the 5’ gain

setName(self, name: bytes | str | String) → None#: Sets the name of the enzyme

setRegEx(self, cleavage_regex: bytes | str | String) → None#: Sets the cleavage regex

setRegExDescription(self, value: bytes | str | String) → None#: Sets the regex description

setSynonyms(self, synonyms: Set[bytes]) → None#: Sets the synonyms

setThreePrimeGain(self, value: bytes | str | String) → None#: Sets the 3’ gain

setValueFromFile(self, key: bytes | str | String, value: bytes | str | String) → bool#: Sets the value of a member variable based on an entry from an input file