Implement tool to merge metadata excel sheet into MSP by joining on a specified column/metadata key

[hechth]

The tool should take an msp file and a tabular file and the metadata in the tabular file should be joined with the metadata in the MSP file on a user specified column.

The output should be the MSP file with the attached metadata.

example code

import pandas
import matchms
import numpy as np
matchms.set_matchms_logger_level('ERROR')

msp_file= "example.msp"
metadata_table_file = "metadata.csv"

spectra= list(matchms.importing.load_from_msp(msp_file))

metadata_table= pandas.read_csv(metadata_table_file )

# postprocessing
metadata_table.set_index('compound_name', inplace=True)
metadata_table.drop_duplicates(inplace=True)

spectra_metadata= pandas.DataFrame.from_dict([x.metadata for x in spectra])
spectra_metadata.reset_index(inplace=True)
spectra_metadata.set_index('compound_name', inplace=True)

merged = metadata_table.join(spectra_metadata, how='inner')

spectra_arr = np.asarray(spectra, dtype=object)

def update_metadata(spectrum:matchms.Spectrum , row):
    spectrum.metadata.update(row.to_dict())
    return spectrum

vec_update_metadata = np.vectorize(update_metadata)
merged_array= vec_update_metadata (spectra_arr, merged)

matchms.exporting.save_as_msp(merged_array.tolist(), "merged.msp")

matchms_metadata_merge_testdata.zip

EDIT 16.11.2024 This is basically solved and only waits for the matchms next release. This then means the package goes to bioconda and we use the newer version of the package in this PR.

[hechth]

xref https://github.com/matchms/matchms/pull/547

[hechth]

this is waiting for a new matchms release which will include the functionality