OSWReader

class pyprophet.io.ipf.osw.OSWReader(config: IPFIOConfig)[source]

Bases: BaseOSWReader

Class for reading and processing data from an OpenSWATH workflow OSW-sqlite based file.

The OSWReader class provides methods to read different levels of data from the file and process it accordingly. It supports reading data for semi-supervised learning, IPF analysis, context level analysis.

infile

Input file path.

Type:: str

outfile

Output file path.

Type:: str

classifier

Classifier used for semi-supervised learning.

Type:: str

level

Level used in semi-supervised learning (e.g., ‘ms1’, ‘ms2’, ‘ms1ms2’, ‘transition’, ‘alignment’), or context level used peptide/protein/gene inference (e.g., ‘global’, ‘experiment-wide’, ‘run-specific’).

Type:: str

glyco

Flag indicating whether analysis is glycoform-specific.

Type:: bool

read()[source]: Read data from the input file based on the alogorithm.

__init__(config: IPFIOConfig)[source]

Initialize the reader with a given configuration.

Parameters:: config (BaseIOConfig) – Configuration object containing input details, and module specific config for params for reading.

_create_indexes()[source]: Always use a temporary SQLite connection to create indexes directly on the .osw file, since DuckDB doesn’t seem to currently support creating indexes on attached SQLite databases.

read(level: Literal['peakgroup_precursor', 'transition', 'alignment']) → DataFrame[source]: Abstract method to be implemented by subclasses to read data from OSW format for a specific algorithm.