update: psm

quantmsio/commands/psm_command.py

@@ -26,6 +26,11 @@
     required=False,
     is_flag=True,
 )
+@click.option(
+    "--protein_file",
+    help="the mzTab file, this will be used to extract the protein information",
+    required=False,
+)
 @click.option(
     "--output_prefix_file",
     help="Prefix of the parquet file needed to generate the file name",
@@ -36,6 +41,7 @@ def convert_psm_file(
     mztab_file: str,
     output_folder: str,
     use_cache: bool,
+    protein_file:str=None,
     output_prefix_file: str = None,
     verbose: bool = False,
 ):
@@ -61,6 +67,7 @@ def convert_psm_file(
         parquet_path=psm_manager.parquet_path,
         verbose=verbose,
         use_cache=use_cache,
+        protein_file=protein_file,
     )
 
 

quantmsio/core/psm.py

@@ -172,6 +172,7 @@ def convert_mztab_to_psm(
         parquet_path: str = None,
         verbose: bool = False,
         batch_size: int = 100000,
+        protein_file=None,
         use_cache: bool = False,
     ):
         """
@@ -221,7 +222,7 @@ def convert_mztab_to_psm(
             logger.info("The parquet file was generated in: {}".format(self.parquet_path))
         else:
             convert = PsmInMemory(self.schema)
-            convert.write_feature_to_file(mztab_path, self.parquet_path, chunksize=batch_size)
+            convert.write_feature_to_file(mztab_path, self.parquet_path, chunksize=batch_size,protein_file=protein_file)
             logger.info("The parquet file was generated in: {}".format(self.parquet_path))
 
     @staticmethod