OSWFile Class Reference

This class serves for reading in and writing OpenSWATH OSW files. More...

#include <OpenMS/FORMAT/OSWFile.h>

Collaboration diagram for OSWFile:

Classes
struct	PercolatorFeature

Public Types
enum class	OSWLevel { MS1 , MS2 , TRANSITION , SIZE_OF_OSWLEVEL }
	for Percolator data read/write operations More...

Public Member Functions
	OSWFile (const std::string &filename)
	OSWFile (const OSWFile &rhs)=default
OSWFile &	operator= (const OSWFile &rhs)=default
void	read (OSWData &swath_result)
void	readMinimal (OSWData &swath_result)
void	readProtein (OSWData &swath_result, const Size index)
	populates a protein at index index within swath_results with Peptides, unless the protein already has peptides
std::vector< IPFPrecursorRow >	readIPFPrecursorData (const PeptidoformInferenceConfig &config) const
	Read peakgroup and precursor evidence required for peptidoform inference.
std::vector< IPFTransitionRow >	readIPFTransitionData (const PeptidoformInferenceConfig &config) const
	Read transition-level evidence required for peptidoform inference.
std::vector< IPFAlignmentRow >	readIPFAlignmentData (const PeptidoformInferenceConfig &config) const
	Read alignment-group membership required for optional across-run signal propagation from FEATURE_MS2_ALIGNMENT_CANDIDATE.
std::vector< IPFAlignmentRow >	readIPFAlignmentData (double ipf_max_alignment_pep) const
	Historical overload that reads legacy alignment-group membership from FEATURE_MS2_ALIGNMENT + SCORE_ALIGNMENT.
void	writeIPFResults (const std::string &output_filename, const std::vector< IPFResultRow > &results) const
	Write peptidoform inference results into SCORE_IPF, copying to output_filename first if requested.
std::vector< LevelContextInputRow >	readLevelContextData (InferenceLevel level, InferenceContext context) const
	Read compact peptide-, protein-, or gene-level rows for context inference.
void	writeLevelContextResults (const std::string &output_filename, InferenceLevel level, InferenceContext context, const std::vector< LevelContextResultRow > &results) const
	Write context inference results into SCORE_PEPTIDE / SCORE_PROTEIN / SCORE_GENE.
std::vector< OpenSwathExportRow >	readOpenSwathExportRows (const OpenSwathExportFilterConfig &config) const
	Read filtered feature rows for user-facing OpenSWATH results and matrix exports.
OpenSwathFeatureScoreTable	readOpenSwathFeatureScoreTable (const OpenSwathParquetExportConfig &config) const
	Read scored feature rows for OpenSWATH Parquet export.
OpenSwathTransitionScoreTable	readOpenSwathTransitionScoreTable (const OpenSwathParquetExportConfig &config) const
	Read optional transition-level score rows for OpenSWATH Parquet export.
std::map< Int64, std::string >	readRunBasenames () const
	Read RUN IDs and convert their filenames to user-facing basenames.
UInt64	getRunID () const

Static Public Member Functions
static void	readToPIN (const std::string &filename, const OSWFile::OSWLevel osw_level, std::ostream &pin_output, const double ipf_max_peakgroup_pep, const double ipf_max_transition_isotope_overlap, const double ipf_min_transition_sn)
	Reads an OSW SQLite file and returns the data on MS1-, MS2- or transition-level as ostream (e.g. stringstream or ofstream).
static void	writeFromPercolator (const std::string &osw_filename, const OSWFile::OSWLevel osw_level, const std::map< std::string, PercolatorFeature > &features)
	Updates an OpenSWATH OSW SQLite file with the MS1-, MS2- or transition-level results of Percolator.

Static Public Attributes
static constexpr Size	ALL_PROTEINS = -1
	query all proteins, not just one with a particular ID
static const std::array< std::string,(Size) OSWLevel::SIZE_OF_OSWLEVEL >	names_of_oswlevel

Protected Member Functions
void	readTransitions_ (OSWData &swath_result)
void	getFullProteins_ (OSWData &swath_result, Size prot_index=ALL_PROTEINS)
	fill one (prot_id) or all proteins into swath_result
void	readMeta_ (OSWData &data)
	set source file and sqMass run-ID

Private Attributes
std::string	filename_
	sql file to open/write to
SqliteConnector	conn_
	SQL connection. Stays open as long as this object lives.
bool	has_SCOREMS2_
	database contains pyProphet's score_MS2 table with qvalues

Detailed Description

This class serves for reading in and writing OpenSWATH OSW files.

See OpenSwathOSWWriter for more functionality.

The reader and writer returns data in a format suitable for PercolatorAdapter. OSW files have a flexible data structure. They contain all peptide query parameters of TraML/PQP files with the detected and quantified features of OpenSwathWorkflow (feature, feature_ms1, feature_ms2 & feature_transition).

The OSWFile reader extracts the feature information from the OSW file for each level (MS1, MS2 & transition) separately and generates Percolator input files. For each of the three Percolator reports, OSWFile writer adds a table (score_ms1, score_ms2, score_transition) with the respective confidence metrics. These tables can be mapped to the corresponding feature tables, are very similar to PyProphet results and can thus be used interchangeably.

Member Enumeration Documentation

OSWLevel

enum class OSWLevel

strong

for Percolator data read/write operations

Enumerator
MS1
MS2
TRANSITION
SIZE_OF_OSWLEVEL

Constructor & Destructor Documentation

OSWFile() [1/2]

OSWFile

(

const std::string &

filename

)

opens an OSW file for reading.

Exceptions

Exception::FileNotReadable

if filename does not exist

OSWFile() [2/2]

OSWFile ( const OSWFile &  rhs )

default

Member Function Documentation

getFullProteins_()

void getFullProteins_ ( OSWData &  swath_result, Size  prot_index = ALL_PROTEINS  )

protected

fill one (prot_id) or all proteins into swath_result

Parameters

[out]	swath_result	Output data. Proteins are cleared before if ALL_PROTEINS is used.
[in]	prot_index	Using ALL_PROTEINS queries all proteins (could take some time)

getRunID()

UInt64 getRunID

(

)

const

extract the RUN::ID from the sqMass file

Exceptions

Exception::SqlOperationFailed

more than on run exists

operator=()

OSWFile & operator= ( const OSWFile &  rhs )

default

read()

void read

(

OSWData &

swath_result

)

read data from an SQLLite OSW file into swath_result Depending on the number of proteins, this could take a while.

Note

If you just want the proteins and transitions without peptides and features, use readMinimal().

readIPFAlignmentData() [1/2]

std::vector< IPFAlignmentRow > readIPFAlignmentData

(

const PeptidoformInferenceConfig &

config

)

const

Read alignment-group membership required for optional across-run signal propagation from FEATURE_MS2_ALIGNMENT_CANDIDATE.

readIPFAlignmentData() [2/2]

std::vector< IPFAlignmentRow > readIPFAlignmentData

(

double

ipf_max_alignment_pep

)

const

Historical overload that reads legacy alignment-group membership from FEATURE_MS2_ALIGNMENT + SCORE_ALIGNMENT.

readIPFPrecursorData()

std::vector< IPFPrecursorRow > readIPFPrecursorData

(

const PeptidoformInferenceConfig &

config

)

const

Read peakgroup and precursor evidence required for peptidoform inference.

readIPFTransitionData()

std::vector< IPFTransitionRow > readIPFTransitionData

(

const PeptidoformInferenceConfig &

config

)

const

Read transition-level evidence required for peptidoform inference.

readLevelContextData()

std::vector< LevelContextInputRow > readLevelContextData	(	InferenceLevel	level,
		InferenceContext	context
	)		const

Read compact peptide-, protein-, or gene-level rows for context inference.

readMeta_()

void readMeta_ ( OSWData &  data )

protected

set source file and sqMass run-ID

readMinimal()

void readMinimal

(

OSWData &

swath_result

)

Reads in transitions and a list of protein names/IDs but no peptide/feature/transition mapping data (which could be very expensive). Use in conjunction with on-demand readProtein() to fully populate proteins with peptide/feature data as needed.

Note

If you read in all proteins afterwards in one go anyway, using the read() method will be faster (by about 30%)

readOpenSwathExportRows()

std::vector< OpenSwathExportRow > readOpenSwathExportRows

(

const OpenSwathExportFilterConfig &

config

)

const

Read filtered feature rows for user-facing OpenSWATH results and matrix exports.

readOpenSwathFeatureScoreTable()

OpenSwathFeatureScoreTable readOpenSwathFeatureScoreTable

(

const OpenSwathParquetExportConfig &

config

)

const

Read scored feature rows for OpenSWATH Parquet export.

readOpenSwathTransitionScoreTable()

OpenSwathTransitionScoreTable readOpenSwathTransitionScoreTable

(

const OpenSwathParquetExportConfig &

config

)

const

Read optional transition-level score rows for OpenSWATH Parquet export.

readProtein()

void readProtein	(	OSWData &	swath_result,
		const Size	index
	)

populates a protein at index index within swath_results with Peptides, unless the protein already has peptides

Internally uses the proteins ID to search for cross referencing peptides and transitions in the OSW file.

Parameters

[in]	swath_result	OSWData obtained from the readMinimal() method
[out]	index	Index into swath_result.getProteins()[index]. Make sure the index is within the vector's size.

Exceptions

Exception::InvalidValue

if the protein at index does not have any peptides present in the OSW file

readRunBasenames()

std::map< Int64, std::string > readRunBasenames

(

)

const

Read RUN IDs and convert their filenames to user-facing basenames.

The returned names are stripped to stem names when possible, so sample.mzML.gz becomes sample.

readToPIN()

static void readToPIN ( const std::string &  filename, const OSWFile::OSWLevel  osw_level, std::ostream &  pin_output, const double  ipf_max_peakgroup_pep, const double  ipf_max_transition_isotope_overlap, const double  ipf_min_transition_sn  )

static

Reads an OSW SQLite file and returns the data on MS1-, MS2- or transition-level as ostream (e.g. stringstream or ofstream).

readTransitions_()

void readTransitions_ ( OSWData &  swath_result )

protected

populate transitions of swath_result

Clears swath_result entirely (incl. proteins) before adding transitions.

writeFromPercolator()

static void writeFromPercolator ( const std::string &  osw_filename, const OSWFile::OSWLevel  osw_level, const std::map< std::string, PercolatorFeature > &  features  )

static

Updates an OpenSWATH OSW SQLite file with the MS1-, MS2- or transition-level results of Percolator.

writeIPFResults()

void writeIPFResults	(	const std::string &	output_filename,
		const std::vector< IPFResultRow > &	results
	)		const

Write peptidoform inference results into SCORE_IPF, copying to output_filename first if requested.

writeLevelContextResults()

void writeLevelContextResults	(	const std::string &	output_filename,
		InferenceLevel	level,
		InferenceContext	context,
		const std::vector< LevelContextResultRow > &	results
	)		const

Write context inference results into SCORE_PEPTIDE / SCORE_PROTEIN / SCORE_GENE.

Member Data Documentation

ALL_PROTEINS

constexpr Size ALL_PROTEINS = -1

staticconstexpr

query all proteins, not just one with a particular ID

conn_

SqliteConnector conn_

private

SQL connection. Stays open as long as this object lives.

filename_

std::string filename_

private

sql file to open/write to

has_SCOREMS2_

bool has_SCOREMS2_

private

database contains pyProphet's score_MS2 table with qvalues

names_of_oswlevel

const std::array<std::string, (Size)OSWLevel::SIZE_OF_OSWLEVEL> names_of_oswlevel

static