OSWReader
- class pyprophet.io.scoring.osw.OSWReader(config: RunnerIOConfig)[source]
Bases:
BaseOSWReaderClass 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
- __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.
- _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.
- _get_precursor_filter_clause()[source]
Return a WHERE/AND clause fragment for filtering by sampled precursor IDs when subsampling is enabled. Returns empty string if no subsampling, otherwise returns a clause like: “ AND f.PRECURSOR_ID IN (SELECT PRECURSOR_ID FROM sampled_precursor_ids)”
- _read_using_duckdb(con)[source]
Read features from SQLite using DuckDB based on the specified level.
Parameters: - con: Connection to the DuckDB database.
Returns: - Features based on the specified level.
Raises: - click.ClickException: If the specified level is unsupported.