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) → Union[bytes, str, String]: Returns the boundary used for the MIME format

getCharges(self) → Union[bytes, str, String]: Returns the charges

getCleavage(self) → Union[bytes, str, String]: Returns the enzyme used for cleavage

getDB(self) → Union[bytes, str, String]: Returns the DB to use

getFormVersion(self) → Union[bytes, str, String]: Returns the Mascot form version

getHits(self) → Union[bytes, str, String]: Returns the number of hits to report back

getInstrument(self) → Union[bytes, str, String]: Returns the instrument type

getLogType(self) → int: Returns the type of progress log being used

getMassType(self) → Union[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) → Union[bytes, str, String]: Returns the search type

getTaxonomy(self) → Union[bytes, str, String]: Returns the taxonomy

getVariableModifications(self) → List[bytes]: Returns a vector containing the variable modifications (default none)

load(self, filename: Union[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: Union[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: Union[bytes, str, String]) → None: Sets the enzyme used for cleavage (default Trypsin). See mascot path /config/enzymes for possible settings

setDB(self, db: Union[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: Union[bytes, str, String]) → None: Sets the Mascot form version (default 1.01)

setHits(self, hits: Union[bytes, str, String]) → None: Sets the number of hits to report back (default 20)

setInstrument(self, instrument: Union[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: Union[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: Union[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: Union[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: Union[bytes, str, String]) → None

store()

Overload:

store(self, filename: Union[bytes, str, String], spec: MSSpectrum, mz: float, retention_time: float, search_title: Union[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: Union[bytes, str, String], experiment: MSExperiment, search_title: Union[bytes, str, String]) → None

Stores the experiment data in a MascotInfile that can be used as input for MASCOT shell execution