MascotInfile#
- class pyopenms.MascotInfile#
Bases:
object
Cython implementation of _MascotInfile
- Original C++ documentation is available here
– Inherits from [‘ProgressLogger’]
- __init__()#
Overload:
- __init__(self) None
Overload:
- __init__(self, in_0: MascotInfile) None
Methods
Overload:
endProgress
(self)Ends the progress display
getBoundary
(self)Returns the boundary used for the MIME format
getCharges
(self)Returns the charges
getCleavage
(self)Returns the enzyme used for cleavage
getDB
(self)Returns the DB to use
getFormVersion
(self)Returns the Mascot form version
getHits
(self)Returns the number of hits to report back
getInstrument
(self)Returns the instrument type
getLogType
(self)Returns the type of progress log being used
getMassType
(self)Returns the used mass type ("Monoisotopic" or "Average")
getMissedCleavages
(self)Returns the number of allowed missed cleavages
getModifications
(self)Returns a vector containing the fixed modifications (default none)
getPeakMassTolerance
(self)Returns the peak mass tolerance in Da
Returns the precursor mass tolerance
getSearchType
(self)Returns the search type
getTaxonomy
(self)Returns the taxonomy
getVariableModifications
(self)Returns a vector containing the variable modifications (default none)
load
(self, filename, exp)Loads a Mascot Generic File into a PeakMap
nextProgress
(self)Increment progress by 1 (according to range begin-end)
setBoundary
(self, boundary)Sets the boundary used for the MIME format.By default a 22 character random string is used
setCharges
(self, charges)Sets the charges (default 1+, 2+ and 3+)
setCleavage
(self, cleavage)Sets the enzyme used for cleavage (default Trypsin).
setDB
(self, db)Sets the DB (default MSDB).
setFormVersion
(self, form_version)Sets the Mascot form version (default 1.01)
setHits
(self, hits)Sets the number of hits to report back (default 20)
setInstrument
(self, instrument)Sets the instrument type (Default Default).
setLogType
(self, in_0)Sets the progress log that should be used.
setMassType
(self, mass_type)Sets the used mass type "Monoisotopic" or "Average" (default Monoisotopic)
setMissedCleavages
(self, missed_cleavages)Sets the number of allowed missed cleavages (default 1)
setModifications
(self, mods)Sets the fixed modifications (default none).
setPeakMassTolerance
(self, ion_mass_tolerance)Sets the peak mass tolerance in Da (default 1.0)
setPrecursorMassTolerance
(self, ...)Sets the precursor mass tolerance in Da (default 2.0)
setProgress
(self, value)Sets the current progress
setSearchType
(self, search_type)Sets the search type (default MIS).
setTaxonomy
(self, taxonomy)Sets the taxonomy (default All entries).
setVariableModifications
(self, mods)Sets the fixed modifications (default none).
startProgress
(self, begin, end, label)Overload:
- endProgress(self) None #
Ends the progress display
- getLogType(self) int #
Returns the type of progress log being used
- getMissedCleavages(self) int #
Returns the number of allowed missed cleavages
- getModifications(self) List[bytes] #
Returns a vector containing the fixed modifications (default none)
- getPeakMassTolerance(self) float #
Returns the peak mass tolerance in Da
- getPrecursorMassTolerance(self) float #
Returns the precursor mass tolerance
- getVariableModifications(self) List[bytes] #
Returns a vector containing the variable modifications (default none)
- load(self, filename: bytes | str | String, exp: MSExperiment) None #
Loads a Mascot Generic File into a PeakMap
- Parameters:
filename – File name which the map should be read from
exp – The map which is filled with the data from the given file
- Raises:
Exception: FileNotFound is thrown if the given file could not be found
- nextProgress(self) None #
Increment progress by 1 (according to range begin-end)
- setBoundary(self, boundary: bytes | str | String) None #
Sets the boundary used for the MIME format.By default a 22 character random string is used
- setCharges(self, charges: List[int]) None #
Sets the charges (default 1+, 2+ and 3+)
- setCleavage(self, cleavage: bytes | str | String) None #
Sets the enzyme used for cleavage (default Trypsin). See mascot path /config/enzymes for possible settings
- setDB(self, db: bytes | str | String) None #
Sets the DB (default MSDB). See mascot path /config/mascot.dat in “Databases” section for possible settings
- setFormVersion(self, form_version: bytes | str | String) None #
Sets the Mascot form version (default 1.01)
- setHits(self, hits: bytes | str | String) None #
Sets the number of hits to report back (default 20)
- setInstrument(self, instrument: bytes | str | String) None #
Sets the instrument type (Default Default). Possible instruments are ESI-QUAD-TOF, MALDI-TOF-PSD, ESI-TRAP, ESI-QUAD, ESI-FTICR, MALDI-TOF-TOF, ESI-4SECTOR, FTMS-ECD, MALDI-QUAD-TOF, MALDI-QIT-TOF
- setLogType(self, in_0: int) None #
Sets the progress log that should be used. The default type is NONE!
- setMassType(self, mass_type: bytes | str | String) None #
Sets the used mass type “Monoisotopic” or “Average” (default Monoisotopic)
- setMissedCleavages(self, missed_cleavages: int) None #
Sets the number of allowed missed cleavages (default 1)
- setModifications(self, mods: List[bytes]) None #
Sets the fixed modifications (default none). See mascot path /config/mod_file for possible settings
- setPeakMassTolerance(self, ion_mass_tolerance: float) None #
Sets the peak mass tolerance in Da (default 1.0)
- setPrecursorMassTolerance(self, precursor_mass_tolerance: float) None #
Sets the precursor mass tolerance in Da (default 2.0)
- setProgress(self, value: int) None #
Sets the current progress
- setSearchType(self, search_type: bytes | str | String) None #
Sets the search type (default MIS). So far only MIS is supported!Valid types are “MIS” (MS/MS Ion Search), “PMF” (Peptide Mass Fingerprint) , “SQ” (Sequence Query)
- setTaxonomy(self, taxonomy: bytes | str | String) None #
Sets the taxonomy (default All entries). See mascot path /config/taxonomy for possible settings
- setVariableModifications(self, mods: List[bytes]) None #
Sets the fixed modifications (default none). See mascot path /config/mod_file for possible settings
- store()#
Overload:
- store(self, filename: bytes | str | String, spec: MSSpectrum, mz: float, retention_time: float, search_title: bytes | str | String) None
Stores the peak list in a MascotInfile that can be used as input for MASCOT shell execution
Overload:
- store(self, filename: bytes | str | String, experiment: MSExperiment, search_title: bytes | str | String) None
Stores the experiment data in a MascotInfile that can be used as input for MASCOT shell execution