import logging
import os
import pickle
from matchms.exporting import save_as_json, save_as_mgf, save_as_msp
from matchms.Spectrum import Spectrum
from matchms.utils import filter_empty_spectra
logger = logging.getLogger("matchms")
[docs]
def save_spectra(
spectra: list[Spectrum],
file: str,
export_style: str = "matchms",
append: bool = False,
) -> None:
"""Saves spectra as the file type specified.
The following file extensions can be used: .json, .mgf, and .msp.
Args:
-----
spectra:
The spectra that are saved.
file:
Path to file containing spectra, with file extension ".json", ".mgf", ".msp".
export_style:
Converts the keys to the required export style.
One of ["matchms", "massbank", "nist", "riken", "gnps"]. Default is "matchms".
append:
Only supported for ".mgf", and ".msp" filetypes. If True, will try to append
to an existing file, instead of creating a new file. Default is `False`.
"""
if os.path.exists(file) and not append:
raise FileExistsError(f"The specified file: {file} already exists.")
ftype = os.path.splitext(file)[1].lower()[1:]
if append and ftype not in ("mgf", "msp"):
raise ValueError(f"{ftype} isn't supported for when `append` is True")
if not isinstance(spectra, list):
spectra = [spectra]
if len(spectra) == 0:
logger.warning("No spectra to save. File will be empty.")
with open(file, "w", encoding="utf-8"):
pass
return
if ftype == "json":
save_as_json(spectra, file, export_style)
elif ftype == "mgf":
file_mode = "a" if append else "w"
save_as_mgf(spectra, file, export_style, file_mode=file_mode)
elif ftype == "msp":
file_mode = "a" if append else "w"
save_as_msp(spectra, file, style=export_style, file_mode=file_mode)
elif ftype == "pickle":
if export_style != "matchms":
logger.error(
"The only available export style for pickle is 'matchms', your export style %s",
export_style,
)
save_as_pickled_file(spectra, file)
else:
raise TypeError(f"File extension of file: {file} is not recognized")
[docs]
def save_as_pickled_file(spectra, filename: str) -> None:
"""Stores spectra as a pickled object
Args:
-----
spectra:
The spectra that are saved.
filename:
Path to file containing spectra, with file extension "json", "mgf", "msp"
"""
if os.path.exists(filename):
raise FileExistsError(f"The file '{filename}' already exists.")
if not isinstance(spectra, list):
raise TypeError("Expected list of spectra")
if not isinstance(spectra[0], Spectrum):
raise TypeError("Expected list of spectra")
spectra = filter_empty_spectra(spectra)
with open(filename, "wb") as f:
pickle.dump(spectra, f)