OSWWriter

class pyprophet.io.export.osw.OSWWriter(config: ExportIOConfig)

Bases: BaseOSWWriter

Class for writing OpenSWATH results to various formats.

__init__(config: ExportIOConfig)

Initialize the writer with a given configuration.

Parameters:

config (BaseIOConfig) – Configuration object containing output details.

_build_combined_precursor_query(conn, column_info: dict) → str

Build combined precursor query for single file export

_build_combined_transition_query(column_info: dict) → str

Build combined transition query for single file export

_build_gene_joins(column_info: dict) → str

Build gene join clauses if gene tables exist

_build_precursor_query(conn, column_info: dict) → str

Build SQL query for precursor data

_build_score_column_selection_and_joins(column_info: dict) → Tuple[str, str, str]

Build score column selection and joins based on available score tables

_build_transition_query(column_info: dict) → str

Build SQL query for transition data

_build_transition_score_columns_and_join(column_info: dict) → Tuple[str, str]

Build score columns and join clause for transition scores

_check_contexts(conn, score_table) → list

Get list of contexts available in score table

_convert_to_single_parquet() → None

Convert OSW to single parquet file

_convert_to_split_parquet() → None

Convert OSW to split parquet format

_create_temp_table(conn, column_info: dict) → None

Create temporary table with combined schema

_create_unimod_to_codename_peptide_id_mapping_table() → None

Create peptide unimod to codename mapping table in SQLite database.

_export_alignment_data(conn, path: str | None = None) → None

Export feature alignment data with scores if available

_export_combined(conn, column_info: dict) → None

Export combined data (all runs together)

_export_single_file(conn, column_info: dict) → None

Export all data to a single parquet file

_export_split_by_run(conn, column_info: dict) → None

Export data split by run into separate directories

_get_peptide_protein_score_table(level, contexts: list) → str

Create a DuckDB view for peptide/protein score data and return the view name

_insert_precursor_peptide_ipf_map() → None

Insert precursor-peptide-IPF table into the input sqlite OSW file.

_prepare_column_info(conn) → dict

Prepare column information and table checks

_register_peptide_ipf_map(conn: DuckDBPyConnection) → None

Create or refresh peptide ↔ IPF peptide mapping inside DuckDB.

_write_parquet() → None

Handle parquet export based on configuration

export() → None

Main entry point for writing data based on configured format