RNaseDigestion

class pyopenms.RNaseDigestion

Bases: object

Cython implementation of _RNaseDigestion

Original C++ documentation is available here

– Inherits from [‘EnzymaticDigestion’]

Class for the enzymatic digestion of RNA

Usage:

from pyopenms import *
oligo = NASequence.fromString("pAUGUCGCAG");

dig = RNaseDigestion()
dig.setEnzyme("RNase_T1")

result = []
dig.digest(oligo, result)
for fragment in result:
  print (fragment)
__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: RNaseDigestion) → None

Methods

__init__

Overload:

countInternalCleavageSites(self, sequence)

Returns the number of internal cleavage sites for this sequence.

digest

Overload:

digestUnmodified(self, sequence, output, ...)

Performs the enzymatic digestion of an unmodified sequence

getEnzymeName(self)

Returns the enzyme for the digestion

getMissedCleavages(self)

Returns the max.

getSpecificity(self)

Returns the specificity for the digestion

getSpecificityByName(self, name)

Returns the specificity by name.

isValidProduct(self, sequence, pos, length, ...)

Boolean operator returns true if the peptide fragment starting at position pos with length length within the sequence sequence generated by the current enzyme

setEnzyme

Overload:

setMissedCleavages(self, missed_cleavages)

Sets the max.

setSpecificity(self, spec)

Sets the specificity for the digestion (default is SPEC_FULL)
countInternalCleavageSites(self, sequence: Union[bytes, str, String]) → int

Returns the number of internal cleavage sites for this sequence.

digest()

Overload:

digest(self, rna: NASequence, output: List[NASequence]) → None

Overload:

digest(self, rna: NASequence, output: List[NASequence], min_length: int, max_length: int) → None

Performs the enzymatic digestion of a (potentially modified) RNA

Parameters

  • rna – Sequence to digest

  • output – Digestion productsq

  • min_length – Minimal length of reported products

  • max_length – Maximal length of reported products (0 = no restriction)

Returns

Number of discarded digestion products (which are not matching length restrictions)

Overload:

digest(self, id_data: IdentificationData) → None

Overload:

digest(self, id_data: IdentificationData, min_length: int, max_length: int) → None

Performs the enzymatic digestion of all RNA parent molecules in IdentificationData (id_data)

Parameters

  • id_data – IdentificationData object which includes sequences to digest

  • min_length – Minimal length of reported products

  • max_length – Maximal length of reported products (0 = no restriction)

Returns

Number of discarded digestion products (which are not matching length restrictions)

digestUnmodified(self, sequence: StringView, output: List[StringView], min_length: int, max_length: int) → int

Performs the enzymatic digestion of an unmodified sequence

By returning only references into the original string this is very fast

Parameters

  • sequence – Sequence to digest

  • output – Digestion products

  • min_length – Minimal length of reported products

  • max_length – Maximal length of reported products (0 = no restriction)

Returns

Number of discarded digestion products (which are not matching length restrictions)

getEnzymeName(self) → Union[bytes, str, String]

Returns the enzyme for the digestion

getMissedCleavages(self) → int

Returns the max. number of allowed missed cleavages for the digestion

getSpecificity(self) → int

Returns the specificity for the digestion

getSpecificityByName(self, name: Union[bytes, str, String]) → int

Returns the specificity by name. Returns SPEC_UNKNOWN if name is not valid

isValidProduct(self, sequence: Union[bytes, str, String], pos: int, length: int, ignore_missed_cleavages: bool) → bool

Boolean operator returns true if the peptide fragment starting at position pos with length length within the sequence sequence generated by the current enzyme

Checks if peptide is a valid digestion product of the enzyme, taking into account specificity and the MC flag provided here

Parameters

  • protein – Protein sequence

  • pep_pos – Starting index of potential peptide

  • pep_length – Length of potential peptide

  • ignore_missed_cleavages – Do not compare MC’s of potential peptide to the maximum allowed MC’s

Returns

True if peptide has correct n/c terminals (according to enzyme, specificity and missed cleavages)

setEnzyme()

Overload:

setEnzyme(self, name: Union[bytes, str, String]) → None

Sets the enzyme for the digestion (by name)

Overload:

setEnzyme(self, enzyme: DigestionEnzyme) → None

Sets the enzyme for the digestion

setMissedCleavages(self, missed_cleavages: int) → None

Sets the max. number of allowed missed cleavages for the digestion (default is 0). This setting is ignored when log model is used

setSpecificity(self, spec: int) → None

Sets the specificity for the digestion (default is SPEC_FULL)