QuantmsIO Class Reference

File adapter for writing PSM (Peptide Spectrum Match) data to parquet files. More...

#include <OpenMS/FORMAT/QuantmsIO.h>

Inheritance diagram for QuantmsIO:

Collaboration diagram for QuantmsIO:

Public Member Functions
	QuantmsIO ()=default
	Default constructor. More...
	~QuantmsIO ()
	Destructor. More...
void	store (const String &filename, const std::vector< ProteinIdentification > &protein_identifications, const PeptideIdentificationList &peptide_identifications)
	Store peptide and protein identifications in parquet format. More...
void	store (const String &filename, const std::vector< ProteinIdentification > &protein_identifications, const PeptideIdentificationList &peptide_identifications, bool export_all_psms)
	Store peptide and protein identifications in parquet format with all PSMs. More...
void	store (const String &filename, const std::vector< ProteinIdentification > &protein_identifications, const PeptideIdentificationList &peptide_identifications, bool export_all_psms, const std::set< String > &meta_value_keys)
	Store peptide and protein identifications in parquet format with enhanced options. More...
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...
virtual	~ProgressLogger ()
	Destructor. More...
	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...
LogType	getLogType () const
	Returns the type of progress log being used. More...
void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. More...
void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...
void	setProgress (SignedSize value) const
	Sets the current progress. More...
void	endProgress (UInt64 bytes_processed=0) const
void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. More...
Protected Attributes inherited from ProgressLogger
LogType	type_
time_t	last_invoke_
ProgressLoggerImpl *	current_logger_
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

File adapter for writing PSM (Peptide Spectrum Match) data to parquet files.

This class converts OpenMS ProteinIdentification and PeptideIdentification objects to parquet format following the quantms.io PSM specification.

The parquet output contains columns following the quantms.io PSM specification:

• sequence: unmodified peptide sequence
• peptidoform: peptide sequence with modifications
• modifications: peptide modifications (null for now)
• precursor_charge: precursor charge
• posterior_error_probability: PEP score from metavalues (nullable)
• is_decoy: decoy flag (0=target, 1=decoy) based on target_decoy metavalue
• calculated_mz: theoretical m/z from sequence
• observed_mz: experimental precursor m/z
• additional_scores: additional scores (null for now)
• protein_accessions: protein accessions (null for now)
• predicted_rt: predicted retention time (null for now)
• reference_file_name: reference file name
• cv_params: CV parameters (null for now)
• scan: scan identifier
• rt: retention time in seconds (nullable)
• ion_mobility: ion mobility value (nullable, null for now)
• number_peaks: number of peaks (nullable, null for now)
• mz_array: m/z values array (null for now)
• intensity_array: intensity values array (null for now)
• file_metadata: file-level metadata with quantmsio_version (1.0), creator (OpenMS), file_type (psm), creation_date (actual timestamp), uuid (generated), scan_format (scan), software_provider (OpenMS)

Only the first peptide hit per peptide identification is processed by default (no rank field). When export_all_psms is enabled, all peptide hits are processed with a rank field. PEP scores are automatically detected from metavalues using known PEP score names. Optional meta value columns can be added for specific keys.

Constructor & Destructor Documentation

QuantmsIO()

QuantmsIO ( )

default

Default constructor.

~QuantmsIO()

~QuantmsIO

(

)

Destructor.

Member Function Documentation

store() [1/3]

void store	(	const String &	filename,
		const std::vector< ProteinIdentification > &	protein_identifications,
		const PeptideIdentificationList &	peptide_identifications
	)

Store peptide and protein identifications in parquet format.

Parameters

filename	Output filename (should end with .parquet)
protein_identifications	Vector of protein identifications
peptide_identifications	Vector of peptide identifications

Exceptions

Exception::UnableToCreateFile

if file cannot be created

store() [2/3]

void store	(	const String &	filename,
		const std::vector< ProteinIdentification > &	protein_identifications,
		const PeptideIdentificationList &	peptide_identifications,
		bool	export_all_psms
	)

Store peptide and protein identifications in parquet format with all PSMs.

Parameters

filename	Output filename (should end with .parquet)
protein_identifications	Vector of protein identifications
peptide_identifications	Vector of peptide identifications
export_all_psms	If true, export all PSMs per spectrum with rank column

Exceptions

Exception::UnableToCreateFile

if file cannot be created

store() [3/3]

void store	(	const String &	filename,
		const std::vector< ProteinIdentification > &	protein_identifications,
		const PeptideIdentificationList &	peptide_identifications,
		bool	export_all_psms,
		const std::set< String > &	meta_value_keys
	)

Store peptide and protein identifications in parquet format with enhanced options.

Parameters

filename	Output filename (should end with .parquet)
protein_identifications	Vector of protein identifications
peptide_identifications	Vector of peptide identifications
export_all_psms	If true, export all PSMs per spectrum with rank column. If false, export only first PSM
meta_value_keys	Set of meta value keys to export as additional columns

Exceptions

Exception::UnableToCreateFile

if file cannot be created