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support reading gzipped spectrum files #226

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support reading gzipped spectrum files #226

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0771b23
add support for gzipped files
paretje Aug 23, 2024
99ace0f
catch exception instead of own filetype check
paretje Aug 23, 2024
06b2e95
drop unused function
paretje Aug 29, 2024
14e4330
update documentation to run ms2pip correlate
paretje Aug 29, 2024
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9 changes: 5 additions & 4 deletions ms2pip/spectrum_input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,11 +29,12 @@ def read_spectrum_file(spectrum_file: str) -> Generator[ObservedSpectrum, None,
If the file extension is not supported.

"""
file_extension = Path(spectrum_file).suffix.lower()
if file_extension not in [".mgf", ".mzml", ".d"] and not _is_minitdf(spectrum_file):
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raise UnsupportedSpectrumFiletypeError(file_extension)
try:
spectra = get_ms2_spectra(str(spectrum_file))
except ValueError:
raise UnsupportedSpectrumFiletypeError(Path(spectrum_file).suffixes)

for spectrum in get_ms2_spectra(str(spectrum_file)):
for spectrum in spectra:
obs_spectrum = ObservedSpectrum(
mz=np.array(spectrum.mz, dtype=np.float32),
intensity=np.array(spectrum.intensity, dtype=np.float32),
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