Fix usage of config file in GUI (was not parsed at all); fix bugs fro…

…m previous commit

ms2rescore/core.py

@@ -37,7 +37,7 @@ def rescore(configuration: Dict, psm_list: Optional[PSMList] = None) -> None:
     logger.debug("Using %i of %i available CPUs.", int(config["processes"]), int(cpu_count()))
 
     # Parse PSMs
-    psm_list = parse_psms(config, psm_list, output_file_root)
+    psm_list = parse_psms(config, psm_list)
 
     # Log #PSMs identified before rescoring
     id_psms_before = _log_id_psms_before(psm_list)

ms2rescore/gui/app.py

@@ -242,7 +242,7 @@ def _parse_modification_mapping(table_output):
         for mod in table_output:
             if mod[0] and mod[1]:
                 modification_map[mod[0].strip()] = mod[1].strip()
-        return modification_map
+        return modification_map or None
 
     @staticmethod
     def _parse_fixed_modifications(table_output):
@@ -252,7 +252,7 @@ def _parse_fixed_modifications(table_output):
             if mod[0] and mod[1]:
                 amino_acids = [aa.upper() for aa in mod[1].strip().split(",")]
                 fixed_modifications[mod[0]] = amino_acids
-        return fixed_modifications
+        return fixed_modifications or None
 
 
 class PSMFileConfigFrame(ctk.CTkFrame):
@@ -612,7 +612,7 @@ def __init__(self, *args, **kwargs):
         self.configure(fg_color="transparent")
         self.grid_columnconfigure(0, weight=1)
 
-        self.title = widgets.Heading(self, text="Percolator configuration")
+        self.title = widgets.Heading(self, text="Percolator coffeeguration")
         self.title.grid(row=0, column=0, columnspan=2, pady=(0, 5), sticky="ew")
 
         self.weights_file = widgets.LabeledFileSelect(
@@ -629,7 +629,7 @@ def get(self) -> Dict:
 def function(config):
     """Function to be executed in a separate process."""
     config = config.copy()
-    config = parse_configurations(config)
+    config = parse_configurations([config["ms2rescore"]["config_file"], config])
     rescore(configuration=config)
 
 

ms2rescore/parse_psms.py

@@ -1,7 +1,7 @@
 import logging
 import re
-from typing import Dict, Union
 from itertools import chain
+from typing import Dict, Union
 
 import psm_utils.io
 from psm_utils import PSMList
@@ -88,7 +88,7 @@ def _read_psms(config, psm_list):
             psm_list_list.append(id_file_psm_list)
             current_file += 1
 
-        return PSMList(psm_list=chain.from_iterable(p.psm_list for p in psm_list_list))
+        return PSMList(psm_list=list(chain.from_iterable(p.psm_list for p in psm_list_list)))
 
 
 def _find_decoys(config, psm_list):
@@ -124,7 +124,7 @@ def _match_psm_ids(old_id, regex_pattern):
     try:
         return match[1]
     except (TypeError, IndexError):
-        raise MS2RescoreError(
+        raise MS2RescoreConfigurationError(
             "`psm_id_pattern` could not be matched to all PSM spectrum IDs."
             " Ensure that the regex contains a capturing group?"
         )

ms2rescore/parse_spectra.py

@@ -65,7 +65,7 @@ def _parse_values_from_mgf(
     )
 
     for spectrum in MGF(str(spectrum_file)):
-        matched_id = spectrum_id_pattern.match(spectrum["id"]).group()
+        matched_id = spectrum_id_pattern.match(spectrum["params"]["title"]).group()
         if missing_rt:
             try:
                 rt_dict[matched_id] = float(spectrum["params"]["rtinseconds"])