IO: Reading and Writing Data
The io module provides tools and utilities for handling input and output operations in PyProphet. It supports various file formats, including SQLite (OSW), Parquet, Split Parquet, and TSV, and provides functionality for reading, writing, and validating data.
Submodules:
util: Contains utility functions for file validation, schema inspection, and logging.
dispatcher: Provides dispatcher classes for routing I/O configurations to the appropriate reader and writer implementations based on file type and context.
_base: Defines abstract base classes and utility methods for implementing custom readers and writers for different data formats.
Dependencies:
pandas
`pyarrow`(optional, for Parquet support)
duckdb
sqlite3
loguru
click
Abstract Base Classes
Abstract base class for implementing readers that load data from different sources (OSW, Parquet, etc.). |
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Abstract base class for implementing writers that save results to various output formats. |
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Class for reading and processing data from an OpenSWATH workflow OSW-sqlite based file. |
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Class for writing OpenSWATH results to an OSW-sqlite based file. |
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Class for reading and processing data from OpenSWATH results stored in Parquet format. |
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Class for writing OpenSWATH results to a Parquet file. |
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Class for reading and processing data from OpenSWATH results stored in a directoy containing split Parquet files. |
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Class for writing OpenSWATH results to a directory containing split Parquet files. |
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Dispatcher class to route I/O configuration to the appropriate reader implementation. |
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Dispatcher class to route I/O configuration to the appropriate writer implementation. |
These submodules provide specific implementations for reading and writing data for specific algorithms.
Scoring
Class for reading and processing data from an OpenSWATH workflow OSW-sqlite based file. |
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Class for writing OpenSWATH results to an OSW-sqlite based file. |
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Class for reading and processing data from OpenSWATH results stored in Parquet format. |
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Class for writing OpenSWATH results to a Parquet file. |
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Class for reading and processing data from OpenSWATH results stored in a directoy containing split Parquet files. |
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Class for writing OpenSWATH results to a directory containing split Parquet files. |
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Class for reading and processing data from OpenSWATH results stored in a tsv format. |
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Class for writing OpenSWATH results to a tsv format. |
IPF
Class for reading and processing data from an OpenSWATH workflow OSW-sqlite based file. |
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Class for writing OpenSWATH results to an OSW-sqlite based file. |
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Class for reading and processing data from OpenSWATH results stored in Parquet format. |
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Class for writing OpenSWATH results to a Parquet file. |
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Class for reading and processing data from OpenSWATH results stored in a directoy containing split Parquet files. |
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Class for writing OpenSWATH results to a directory containing split Parquet files. |
Levels Context
Class for reading and processing data from an OpenSWATH workflow OSW-sqlite based file. |
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Class for writing OpenSWATH results to an OSW-sqlite based file. |
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Class for reading and processing data from OpenSWATH results stored in Parquet format. |
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Class for writing OpenSWATH results to a Parquet file. |
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Class for reading and processing data from OpenSWATH results stored in a directoy containing split Parquet files. |
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Class for writing OpenSWATH results to a directory containing split Parquet files. |
Export
Class for reading and processing data from an OpenSWATH workflow OSW-sqlite based file. |
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Class for writing OpenSWATH results to various formats. |
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Class for reading and processing data from an OpenSWATH workflow parquet based file. |
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Class for writing OpenSWATH results to various formats. |
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Class for reading and processing data from an OpenSWATH workflow parquet split based file. |
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Class for writing OpenSWATH results to various formats. |