diff --git a/massql/msql_fileloading.py b/massql/msql_fileloading.py index 48012ad..66ed447 100644 --- a/massql/msql_fileloading.py +++ b/massql/msql_fileloading.py @@ -5,8 +5,9 @@ import numpy as np from tqdm import tqdm +from matchms.importing import load_from_mgf import pymzml -from pyteomics import mzxml, mzml, mgf +from pyteomics import mzxml, mzml import logging logger = logging.getLogger('msql_fileloading') @@ -142,10 +143,10 @@ def load_data(input_filename, cache=None, cache_dir=None, cache_file=None): return ms1_df, ms2_df def _load_data_mgf(input_filename): - reader = mgf.read(input_filename) + file = load_from_mgf(input_filename) ms2mz_list = [] - for i, spectrum in reader: + for i, spectrum in enumerate(file): if len(spectrum.peaks.mz) == 0: continue diff --git a/requirements.txt b/requirements.txt index da36e5e..5f42f88 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,9 +1,10 @@ +pymzml lark>=1.0 pandas pyarrow tqdm py_expression_eval -pymzml +matchms pyteomics psims plotly diff --git a/setup.py b/setup.py index 82772b0..f826d66 100644 --- a/setup.py +++ b/setup.py @@ -28,12 +28,13 @@ ], packages=["massql"], install_requires=[ + "pymzml", "lark-parser", "pandas", "pyarrow", "tqdm", "py_expression_eval", - "pymzml", + "matchms", "pyteomics", "psims", "plotly", diff --git a/tests/test_file_loading.py b/tests/test_file_loading.py index b7bba85..5f554df 100644 --- a/tests/test_file_loading.py +++ b/tests/test_file_loading.py @@ -92,8 +92,7 @@ def main(): #test_waters_load() #test_cache_feather() #test_nocache() - #test_cache_filename() - test_mgf_load() + test_cache_filename() if __name__ == "__main__":