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
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
- getSynonyms(self) Set[bytes] #
Returns the synonyms
- 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
- setSynonyms(self, synonyms: Set[bytes]) None #
Sets the synonyms