TransitionParquetFile Class Reference

Read OpenSwath Parquet library input (.oswpq) into LightTargetedExperiment. More...

#include <OpenMS/ANALYSIS/OPENSWATH/TransitionParquetFile.h>

Public Member Functions
	TransitionParquetFile ()=default
	Default constructor.
	~TransitionParquetFile ()=default
	Default destructor.
void	convertParquetToTargetedExperiment (const String &oswpq_dir, OpenSwath::LightTargetedExperiment &targeted_exp) const
	Read a .oswpq library directory and populate a LightTargetedExperiment.
void	convertLightTargetedExperimentToParquet (const String &oswpq_path, const OpenSwath::LightTargetedExperiment &targeted_exp) const
	Write a LightTargetedExperiment to a .oswpq library (zip file or directory)

Detailed Description

Read OpenSwath Parquet library input (.oswpq) into LightTargetedExperiment.

The Parquet library format is a directory container with separate tables for precursors and transitions. The reader materializes all rows into OpenSwath::LightTargetedExperiment.

The container layout is:

<library>.oswpq
└── library/
    ├── metadata.json
    ├── precursors.parquet
    └── transitions.parquet

The metadata file contains an OpenMS metadata block and QC counts. The new canonical layout (matching OpenSwathOSWParquetWriter) looks like:

{
  "openms": {
    "schema_version": 1,
    "generator": "TransitionParquetFile",
    "openms_version": "<version>",
    "build_time": "<build_time>",
    "tool": {"name": "OpenSwathWorkflow", "version": "<version>"},
    "counts": {
      "proteins": {"total": 0, "target": 0, "decoy": 0},
      "peptides": {"total": 0, "target": 0, "decoy": 0},
      "precursors": {"total": 0, "target": 0, "decoy": 0},
      "compounds": {"total": 0, "target": 0, "decoy": 0},
      "transitions": {"total": 0, "target": 0, "decoy": 0}
    },
    "fragment_type_counts": {
      "target": {"b": 0, "y": 0, "other": 0},
      "decoy": {"b": 0, "y": 0, "other": 0}
    },
    "charge_counts": {
      "precursor": {"target": {"2": 0, "3": 0}, "decoy": {"2": 0, "3": 0}},
      "transition": {"target": {"1": 0, "2": 0}, "decoy": {"1": 0, "2": 0}}
    }
  }
}

Required columns for precursors.parquet:

• precursor_id (int64)
• precursor_mz (float64)
• charge (int32)
• library_rt (float64) Optional columns:
• library_drift_time (float64)
• traml_id (string)
• decoy (bool)
• modified_sequence (string)
• unmodified_sequence (string)
• protein_accessions (string or list<string>)

Required columns for transitions.parquet:

• transition_id (int64)
• precursor_id (int64)
• product_mz (float64)
• charge (int32)
• type (string)
• ordinal (int32)
• detecting (bool)
• identifying (bool)
• quantifying (bool)
• library_intensity (float64)
• decoy (bool) Optional columns:
• traml_id (string)
• annotation (string)

Constructor & Destructor Documentation

TransitionParquetFile()

TransitionParquetFile ( )

default

Default constructor.

~TransitionParquetFile()

~TransitionParquetFile ( )

default

Default destructor.

Member Function Documentation

convertLightTargetedExperimentToParquet()

void convertLightTargetedExperimentToParquet	(	const String &	oswpq_path,
		const OpenSwath::LightTargetedExperiment &	targeted_exp
	)		const

Write a LightTargetedExperiment to a .oswpq library (zip file or directory)

convertParquetToTargetedExperiment()

void convertParquetToTargetedExperiment	(	const String &	oswpq_dir,
		OpenSwath::LightTargetedExperiment &	targeted_exp
	)		const

Read a .oswpq library directory and populate a LightTargetedExperiment.