update

bigbio · Dec 18, 2024 · aac18e2 · aac18e2
1 parent ae65a4d
commit aac18e2
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Showing 2 changed files with 2 additions and 3 deletions.
diff --git a/quantmsio/core/feature.py b/quantmsio/core/feature.py
@@ -24,7 +24,7 @@ def __init__(self, mzTab_path, sdrf_path, msstats_in_path):
 
     def extract_psm_msg(self, chunksize=2000000, protein_str=None):
         P = Psm(self.mztab_path)
-        pep_dict = P.extract_from_pep(chunksize=chunksize)
+        pep_dict = P.extract_from_pep(chunksize=100000, protein_str=protein_str)
         map_dict = {}
         for psm in P.iter_psm_table(chunksize, protein_str):
             for key, df in psm.groupby(["reference_file_name", "peptidoform", "precursor_charge"]):

diff --git a/quantmsio/operate/tools.py b/quantmsio/operate/tools.py
@@ -36,8 +36,7 @@ def generate_psms_of_spectrum(
     """
     pqwriters, pqwriter_no_part, filename = init_save_info(parquet_path)
     p = Query(parquet_path)
-    for _, table in p.iter_file(file_num=file_num):
-        refs = table["reference_file_name"].unique()
+    for refs, table in p.iter_file(file_num=file_num):
         mzml_handlers = {ref: OpenMSHandler() for ref in refs}
         table[["number_peaks", "mz_array", "intensity_array"]] = table[["reference_file_name", "scan"]].apply(
             lambda x: map_spectrum_mz(