BaseParquetReader
- class pyprophet.io._base.BaseParquetReader(config: BaseIOConfig)[source]
Bases:
BaseReaderClass for reading and processing data from OpenSWATH results stored in Parquet format.
The ParquetReader 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.
This assumes that the input file contains precursor and transition data.
- 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
- __eq__(other)
Return self==value.
- __hash__ = None
- __init__(config: BaseIOConfig)[source]
Initialize the reader with a given configuration.
- Parameters:
config (BaseIOConfig) – Configuration object containing input details, and module specific config for params for reading.
- __repr__()
Return repr(self).
- _collapse_ipf_peptide_ids(df)[source]
Collapse IPF peptide IDs to avoid duplicating feature data in the DataFrame.
Parameters: - df (DataFrame): Input DataFrame containing feature data.
Returns: - DataFrame: DataFrame with collapsed IPF peptide IDs.