DigestionEnzymeRNA

class pyopenms.DigestionEnzymeRNA

Bases: object

Cython implementation of _DigestionEnzymeRNA

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1DigestionEnzymeRNA.html

– Inherits from [‘DigestionEnzyme’]

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__()

  • Cython signature: void DigestionEnzymeRNA()

  • Cython signature: void DigestionEnzymeRNA(DigestionEnzymeRNA &)

Methods

__init__

  • Cython signature: void DigestionEnzymeRNA()

addSynonym

Cython signature: void addSynonym(const String & synonym) Adds a synonym

getCutsAfterRegEx

Cython signature: String getCutsAfterRegEx() Returns the "cuts after ..." regular expression

getCutsBeforeRegEx

Cython signature: String getCutsBeforeRegEx() Returns the "cuts before ..." regular expression

getFivePrimeGain

Cython signature: String getFivePrimeGain() Returns the 5' gain

getName

Cython signature: String getName() Returns the name of the enzyme

getRegEx

Cython signature: String getRegEx() Returns the cleavage regex

getRegExDescription

Cython signature: String getRegExDescription() Returns the regex description

getSynonyms

Cython signature: libcpp_set[String] getSynonyms() Returns the synonyms

getThreePrimeGain

Cython signature: String getThreePrimeGain() Returns the 3' gain

setCutsAfterRegEx

Cython signature: void setCutsAfterRegEx(String value) Sets the "cuts after ..." regular expression

setCutsBeforeRegEx

Cython signature: void setCutsBeforeRegEx(String value) Sets the "cuts before ..." regular expression

setFivePrimeGain

Cython signature: void setFivePrimeGain(String value) Sets the 5' gain

setName

Cython signature: void setName(const String & name) Sets the name of the enzyme

setRegEx

Cython signature: void setRegEx(const String & cleavage_regex) Sets the cleavage regex

setRegExDescription

Cython signature: void setRegExDescription(const String & value) Sets the regex description

setSynonyms

Cython signature: void setSynonyms(libcpp_set[String] & synonyms) Sets the synonyms

setThreePrimeGain

Cython signature: void setThreePrimeGain(String value) Sets the 3' gain

setValueFromFile

Cython signature: bool setValueFromFile(String key, String value) Sets the value of a member variable based on an entry from an input file
addSynonym()

Cython signature: void addSynonym(const String & synonym) Adds a synonym

getCutsAfterRegEx()

Cython signature: String getCutsAfterRegEx() Returns the “cuts after …” regular expression

getCutsBeforeRegEx()

Cython signature: String getCutsBeforeRegEx() Returns the “cuts before …” regular expression

getFivePrimeGain()

Cython signature: String getFivePrimeGain() Returns the 5’ gain

getName()

Cython signature: String getName() Returns the name of the enzyme

getRegEx()

Cython signature: String getRegEx() Returns the cleavage regex

getRegExDescription()

Cython signature: String getRegExDescription() Returns the regex description

getSynonyms()

Cython signature: libcpp_set[String] getSynonyms() Returns the synonyms

getThreePrimeGain()

Cython signature: String getThreePrimeGain() Returns the 3’ gain

setCutsAfterRegEx()

Cython signature: void setCutsAfterRegEx(String value) Sets the “cuts after …” regular expression

setCutsBeforeRegEx()

Cython signature: void setCutsBeforeRegEx(String value) Sets the “cuts before …” regular expression

setFivePrimeGain()

Cython signature: void setFivePrimeGain(String value) Sets the 5’ gain

setName()

Cython signature: void setName(const String & name) Sets the name of the enzyme

setRegEx()

Cython signature: void setRegEx(const String & cleavage_regex) Sets the cleavage regex

setRegExDescription()

Cython signature: void setRegExDescription(const String & value) Sets the regex description

setSynonyms()

Cython signature: void setSynonyms(libcpp_set[String] & synonyms) Sets the synonyms

setThreePrimeGain()

Cython signature: void setThreePrimeGain(String value) Sets the 3’ gain

setValueFromFile()

Cython signature: bool setValueFromFile(String key, String value) Sets the value of a member variable based on an entry from an input file