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API Reference: Utils

This document describes the utility functions in wtv.utils.

read_msp

Reads an MSP file and returns metadata and retention time data using matchms.

Parameters

Parameter Type Default Description
msp_file_path str or Path Required Path to the MSP file
retention str "retention_time" Name of the retention field

Returns

  • Tuple[Dict[str, Dict[float, int]], pd.DataFrame]:
  • Dictionary of compound names to ion intensities
  • DataFrame with columns 'Name' and 'RT'

Example

from wtv.utils import read_msp

meta, rt_data = read_msp("input.msp")
print(meta.keys())  # Compound names
print(rt_data)      # Retention times

write_msp

Writes filtered ions to an MSP file.

Parameters

Parameter Type Description
ion_df pd.DataFrame DataFrame containing ion data with 'RT' and 'ion' columns
output_directory Path Directory to save the output MSP file
source_msp_file Path Path to the source MSP file

Example

from pathlib import Path
from wtv.utils import write_msp

write_msp(ion_df, Path("output"), Path("input.msp"))

load_data

Load and prepare data from an MSP file for ion selection.

Parameters

Parameter Type Description
msp_file_path Path Path to the MSP file
mz_min float Minimum m/z value
mz_max float Maximum m/z value

Returns

  • Tuple[pd.DataFrame, pd.DataFrame]: RT_data and ion matrix

create_ion_matrix

Create a matrix of ion intensities with compounds as rows and m/z values as columns.

Parameters

Parameter Type Description
mz_min float Minimum m/z value
mz_max float Maximum m/z value
meta_1 dict Dictionary of compound ion data

Returns

  • pd.DataFrame: Ion intensity matrix

parse_spectra

Parse spectra to create a matrix of ion intensities and a DataFrame of retention times.

Parameters

Parameter Type Default Description
spectra list[Spectrum] Required List of matchms Spectrum objects
retention str "retention_time" Name of the retention field
mz_min float 0 Minimum m/z value
mz_max float 1000 Maximum m/z value

Returns

  • Tuple[pd.DataFrame, pd.DataFrame]: Ion intensity matrix and RT DataFrame

average_rts_for_duplicated_indices

Average the retention times for duplicated compound indices.

Parameters

Parameter Type Description
RT_data pd.DataFrame DataFrame with retention time data

Returns

  • pd.DataFrame: DataFrame with averaged retention times

get_filtered_spectra

Generate filtered spectra based on ion combinations.

Parameters

Parameter Type Description
spectra list[Spectrum] List of Spectrum objects
combinations pd.DataFrame DataFrame with ion combinations

Returns

  • Generator[Spectrum, None, None]: Generator of filtered spectra