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

__init__

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

getPrecursorMassTolerance(self)

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)

store

Overload:

endProgress(self) None#

Ends the progress display

getBoundary(self) bytes | str | String#

Returns the boundary used for the MIME format

getCharges(self) bytes | str | String#

Returns the charges

getCleavage(self) bytes | str | String#

Returns the enzyme used for cleavage

getDB(self) bytes | str | String#

Returns the DB to use

getFormVersion(self) bytes | str | String#

Returns the Mascot form version

getHits(self) bytes | str | String#

Returns the number of hits to report back

getInstrument(self) bytes | str | String#

Returns the instrument type

getLogType(self) int#

Returns the type of progress log being used

getMassType(self) bytes | str | String#

Returns the used mass type (“Monoisotopic” or “Average”)

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

getSearchType(self) bytes | str | String#

Returns the search type

getTaxonomy(self) bytes | str | String#

Returns the taxonomy

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

startProgress(self, begin: int, end: int, label: bytes | str | String) None#
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