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
Overload:
countInternalCleavageSites
(self, sequence)Returns the number of internal cleavage sites for this sequence.
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
Overload:
setMissedCleavages
(self, missed_cleavages)Sets the max.
setSpecificity
(self, spec)Sets the specificity for the digestion (default is SPEC_FULL)
- countInternalCleavageSites(self, sequence: 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)
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)
- 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: bytes | str | String) int #
Returns the specificity by name. Returns SPEC_UNKNOWN if name is not valid
- isValidProduct(self, sequence: 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: 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)