TSVReader

class pyprophet.io.scoring.tsv.TSVReader(config: RunnerIOConfig)[source]

Bases: BaseReader

Class for reading and processing data from OpenSWATH results stored in a tsv format.

The TSVReader class provides methods to read different levels of data from tsv feature format. It supports reading data for semi-supervised learning only.

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: RunnerIOConfig)[source]

Initialize the reader with a given configuration.

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

read() → DataFrame[source]: Abstract method to be implemented by subclasses to read data from a specific format.