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""" |
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MSZ Mass Spectrometry Dataset Loader |
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This dataset contains compressed mass spectrometry data in MSZ format. |
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Requires the 'mscompress' library for loading. |
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Install: pip install mscompress |
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""" |
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import datasets |
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from pathlib import Path |
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from typing import List, Dict, Any |
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_DESCRIPTION = """ |
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Mass spectrometry dataset in compressed MSZ format. |
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""" |
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_HOMEPAGE = "" |
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_LICENSE = "" |
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_DATA_FILES = ['test.msz'] |
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_MS_LEVEL_FILTER = None |
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_GRANULARITY = "spectrum" |
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class MSZDatasetConfig(datasets.BuilderConfig): |
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"""BuilderConfig for MSZ dataset.""" |
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def __init__(self, **kwargs): |
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super(MSZDatasetConfig, self).__init__(**kwargs) |
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class MSZDataset(datasets.GeneratorBasedBuilder): |
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"""MSZ mass spectrometry dataset.""" |
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VERSION = datasets.Version("1.0.0") |
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BUILDER_CONFIGS = [ |
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MSZDatasetConfig( |
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name="default", |
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version=VERSION, |
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description="Default configuration for MSZ dataset", |
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), |
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] |
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DEFAULT_CONFIG_NAME = "default" |
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def _info(self): |
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if _GRANULARITY == "spectrum": |
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features = datasets.Features({ |
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"source_file": datasets.Value("string"), |
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"spectrum_index": datasets.Value("int64"), |
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"scan_number": datasets.Value("int64"), |
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"ms_level": datasets.Value("int32"), |
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"retention_time": datasets.Value("float64"), |
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"num_peaks": datasets.Value("int64"), |
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"mz": datasets.Sequence(datasets.Value("float64")), |
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"intensity": datasets.Sequence(datasets.Value("float64")), |
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}) |
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else: |
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features = datasets.Features({ |
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"file_path": datasets.Value("string"), |
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"file_name": datasets.Value("string"), |
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"num_spectra": datasets.Value("int64"), |
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"file_size_bytes": datasets.Value("int64"), |
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"compression_format": datasets.Value("string"), |
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}) |
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return datasets.DatasetInfo( |
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description=_DESCRIPTION, |
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features=features, |
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homepage=_HOMEPAGE, |
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license=_LICENSE, |
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) |
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def _split_generators(self, dl_manager): |
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"""Download and extract MSZ files""" |
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try: |
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import mscompress |
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except ImportError: |
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raise ImportError( |
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"The mscompress library is required to load this dataset. " |
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"Install it with: pip install mscompress" |
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) |
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data_dir = dl_manager.download_and_extract({ |
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"data": ["data/" + f for f in _DATA_FILES] |
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}) |
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return [ |
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datasets.SplitGenerator( |
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name=datasets.Split.TRAIN, |
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gen_kwargs={ |
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"msz_files": data_dir["data"], |
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}, |
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), |
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] |
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def _generate_examples(self, msz_files: List[str]): |
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"""Generate examples from MSZ files""" |
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import mscompress |
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idx = 0 |
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if _GRANULARITY == "file": |
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for file_path in msz_files: |
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msz = mscompress.read(file_path) |
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yield idx, { |
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"file_path": file_path, |
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"file_name": Path(file_path).name, |
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"num_spectra": len(msz.spectra), |
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"file_size_bytes": msz.size, |
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"compression_format": msz.data_format.mz_original_compression, |
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} |
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idx += 1 |
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else: |
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for file_path in msz_files: |
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msz = mscompress.read(file_path) |
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for spectrum in msz.spectra: |
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if _MS_LEVEL_FILTER and spectrum.ms_level not in _MS_LEVEL_FILTER: |
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continue |
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yield idx, { |
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"source_file": Path(file_path).name, |
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"spectrum_index": spectrum.index, |
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"scan_number": spectrum.scan_number, |
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"ms_level": spectrum.ms_level, |
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"retention_time": spectrum.retention_time, |
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"num_peaks": spectrum.num_peaks, |
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"mz": spectrum.mz.tolist(), |
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"intensity": spectrum.intensity.tolist(), |
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} |
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idx += 1 |
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