Add mokapot integration; write rescoring output to TSV; minor changes

.gitignore

@@ -5,6 +5,9 @@ old_files/
 prepare_pin_files.py
 *.jar
 
+# Ruff
+.ruff_cache/
+
 # Atom remote-sync config
 .remote-sync.json
 
@@ -90,6 +93,7 @@ celerybeat-schedule
 # virtualenv
 venv/
 ENV/
+.venv*/
 
 # Spyder project settings
 .spyderproject
@@ -99,5 +103,4 @@ ENV/
 
 # vscode
 .vscode/
-.pytest_cache/v/cache/nodeids
-.pytest_cache/v/cache/stepwise
+.pytest_cache/

docs/source/userguide/configuration.rst

@@ -26,8 +26,9 @@ denotes the official Unimod name.
 
 To correctly parse the various notations to ProForma, :py:mod:`psm_utils.io` readers
 require :py:obj:`modification_definitions` that map each specific search engine
-modification label to a valid ProForma label. :py:obj:`modification_definitions` is defined as a :py:obj:`list` of :py:obj:`dict`'s.
-Each :py:obj:`dict` should contain the following key-value pairs:
+modification label to a valid ProForma label. :py:obj:`modification_definitions` is defined as a
+:py:obj:`list` of :py:obj:`dict`'s. Each :py:obj:`dict` should contain the following key-value
+pairs:
 
     - ``site``: Amino acids or peptide termini where the modification occurs. Should be
       the IUPAC one-letter code for amino acid residues and `N-term` or `C-term` for

examples/readme.txt

@@ -4,6 +4,6 @@ Raw file converted to MGF with the Compomics ThermoRawFileParser (https://github
 
 Searched with MaxQuant v1.6.2.3 with all parameters as described in the dataset's original article, with FDR-filtering set to 1 (no filtering)
 Also searched with MS-GF+ v2019.02.28
-MS²ReScore tested with Percolator version 3.02.1
+MS²Rescore tested with Percolator version 3.02.1
 
 Fasta file downloaded from https://www.uniprot.org/proteomes/UP000005640 and https://www.thegpm.org/crap/

ms2rescore/__main__.py

@@ -32,8 +32,8 @@
 CONSOLE = Console(record=True)
 
 
-def _build_credits():
-    """Build credits."""
+def _print_credits():
+    """Print software credits to terminal."""
     text = Text()
     text.append("\n")
     text.append("MS²Rescore", style="bold link https://github.com/compomics/ms2rescore")
@@ -45,8 +45,7 @@ def _build_credits():
     )
     text.append("\n")
     text.stylize("cyan")
-    return text
-
+    CONSOLE.print(text)
 
 def _setup_logging(passed_level: str, log_file: Union[str, Path]):
     """Setup logging for writing to log file and Rich Console."""
@@ -146,18 +145,23 @@ def _parse_arguments() -> argparse.Namespace:
 
 def main():
     """Run MS²Rescore command-line interface."""
-    CONSOLE.print(_build_credits())
+    _print_credits()
 
     cli_args = _parse_arguments()
     if cli_args.config_file:
         config = parse_configurations([cli_args.config_file, cli_args])
     else:
         config = parse_configurations(cli_args)
 
-    output_file_root = Path(config["ms2rescore"]["psm_file"]).with_suffix("")
-    _setup_logging(
-        config["ms2rescore"]["log_level"], str(output_file_root) + "-ms2rescore-log.txt"
-    )
+    if config["ms2rescore"]["output_path"]:
+        output_file_root = (
+            Path(config["ms2rescore"]["output_path"])
+            / Path(config["ms2rescore"]["psm_file"]).stem
+        ).as_posix()
+    else:
+        output_file_root = Path(config["ms2rescore"]["psm_file"]).with_suffix("").as_posix()
+
+    _setup_logging(config["ms2rescore"]["log_level"], output_file_root + "-ms2rescore-log.txt")
 
     try:
         ms2rescore = MS2Rescore(configuration=config)

ms2rescore/feature_generators/ms2pip.py

@@ -5,7 +5,6 @@
 import warnings
 from itertools import chain
 from typing import List, Optional, Union
-import math
 
 import numpy as np
 import pandas as pd
@@ -304,7 +303,7 @@ def _calculate_features_single(self, processing_result: ProcessingResult) -> Uni
         features = dict(
             zip(
                 self.feature_names,
-                [0.0 if math.isnan(ft) else ft for ft in feature_values],
+                [0.0 if np.isnan(ft) else ft for ft in feature_values],
             )
         )
 

ms2rescore/gui/app.py

@@ -356,7 +356,7 @@ def __init__(self, *args, **kwargs):
         self.configure(fg_color="transparent")
         self.grid_columnconfigure(0, weight=1)
 
-        self.title = ctk.CTkLabel(self, text="MS²PIP", fg_color="gray30", corner_radius=6)
+        self.title = widgets.Heading(self, text="MS²PIP")
         self.title.grid(row=0, column=0, columnspan=2, pady=(0, 5), sticky="ew")
 
         self.enabled = widgets.LabeledSwitch(self, label="Enable MS²PIP", default=True)
@@ -393,7 +393,7 @@ def __init__(self, *args, **kwargs):
         self.configure(fg_color="transparent")
         self.grid_columnconfigure(0, weight=1)
 
-        self.title = ctk.CTkLabel(self, text="DeepLC", fg_color="gray30", corner_radius=6)
+        self.title = widgets.Heading(self, text="DeepLC")
         self.title.grid(row=0, column=0, columnspan=2, pady=(0, 5), sticky="ew")
 
         self.enabled = widgets.LabeledSwitch(self, label="Enable DeepLC", default=True)
@@ -461,6 +461,7 @@ def function(config):
 
 
 def app():
+    """Start the application."""
     root = Function2CTk(
         sidebar_frame=SideBar,
         config_frame=ConfigFrame,

ms2rescore/gui/function2ctk.py

@@ -230,10 +230,10 @@ def __init__(
         self.stop_callback = stop_callback
         self.stop_button_pressed = False
 
-        self.grid_columnconfigure(0, weight=2)
-        self.grid_columnconfigure(1, weight=1)
+        self.grid_columnconfigure(0, weight=1)
+        self.grid_columnconfigure(1, minsize=140)
 
-        self.progress_bar = ctk.CTkProgressBar(self)  # , width=150)
+        self.progress_bar = ctk.CTkProgressBar(self)
 
         self.start_button = ctk.CTkButton(master=self, command=self._start_callback, text="Start")
         self.stop_button = ctk.CTkButton(master=self, command=self._stop_callback, text="Stop")
@@ -259,7 +259,7 @@ def _start_callback(self):
         self.stop_button.grid(row=0, column=1, sticky="ew")
 
         # Show and activate progress bar
-        self.progress_bar.grid(row=0, column=0, sticky="ew")
+        self.progress_bar.grid(row=0, column=0, sticky="ew", padx=10)
         self.progress_bar.configure(mode="indeterminate")
         self.progress_bar.start()
 

ms2rescore/gui/widgets.py

@@ -7,6 +7,16 @@
 import customtkinter as ctk
 
 
+class Heading(ctk.CTkLabel):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.configure(
+            fg_color=("gray80", "gray30"),
+            text_color=("black", "white"),
+            corner_radius=6,
+        )
+
+
 class LabeledEntry(ctk.CTkFrame):
     def __init__(self, *args, label="Enter text", placeholder_text="Enter text...", **kwargs):
         super().__init__(*args, **kwargs)
@@ -58,10 +68,8 @@ def __init__(self, *args, label="Select option", options=[], default_value=None,
 
         self._radio_buttons = []
         for i, option in enumerate(options):
-            radio_button = ctk.CTkRadioButton(
-                self, text=option, variable=self.value, value=option
-            )
-            radio_button.grid(row=i+1, column=0, padx=0, pady=(0, 5), sticky="w")
+            radio_button = ctk.CTkRadioButton(self, text=option, variable=self.value, value=option)
+            radio_button.grid(row=i + 1, column=0, padx=0, pady=(0, 5), sticky="w")
             self._radio_buttons.append(radio_button)
 
     def get(self):
@@ -316,7 +324,13 @@ def __init__(self, *args, label=None, columns=2, header_labels=["A", "B"], **kwa
         for i, header in enumerate(self.header_labels):
             header_row.grid_columnconfigure(i, weight=1, uniform=self.uniform_hash)
             padx = (0, 5) if i < len(self.header_labels) - 1 else (0, 0)
-            label = ctk.CTkLabel(header_row, text=header, fg_color="gray30", corner_radius=6)
+            label = ctk.CTkLabel(
+                header_row,
+                text=header,
+                fg_color=("gray80", "gray30"),
+                text_color=("black", "white"),
+                corner_radius=6,
+            )
             label.grid(row=0, column=i, padx=padx, sticky="ew")
 
         # Input rows

ms2rescore/ms2rescore_main.py

@@ -10,7 +10,7 @@
 
 from ms2rescore.exceptions import MS2RescoreConfigurationError, MS2RescoreError
 from ms2rescore.feature_generators import FEATURE_GENERATORS
-from ms2rescore.rescoring_engines import percolator
+from ms2rescore.rescoring_engines import mokapot, percolator
 
 logger = logging.getLogger(__name__)
 
@@ -86,6 +86,11 @@ def run(self):
         # Ensure that spectrum IDs are strings (Pydantic 2.0 does not coerce int to str)
         psm_list["spectrum_id"] = [str(spec_id) for spec_id in psm_list["spectrum_id"]]
 
+        # Store values for comparison later
+        psm_data_before = psm_list.to_dataframe()[
+            ["score", "qvalue", "pep", "is_decoy", "rank"]
+        ].copy()
+
         # Add rescoring features
         feature_names = dict()
         for fgen_name, fgen_config in self.config["feature_generators"].items():
@@ -114,6 +119,7 @@ def run(self):
             logging.debug(f"Creating USIs for {len(psm_list)} PSMs")
             psm_list["spectrum_id"] = [psm.get_usi(as_url=False) for psm in psm_list]
 
+        # Rescore PSMs
         if "percolator" in self.config["rescoring_engine"]:
             percolator.rescore(
                 psm_list,
@@ -124,7 +130,31 @@ def run(self):
             )
 
         elif "mokapot" in self.config["rescoring_engine"]:
-            raise NotImplementedError()
+            mokapot.rescore(psm_list, mokapot_kwargs=self.config["rescoring_engine"]["mokapot"])
+
+        psm_data_after = psm_list.to_dataframe()[
+            ["score", "qvalue", "pep", "is_decoy", "rank"]
+        ].copy()
+
+        # Compare results
+        id_psms_before = (
+            (psm_data_before["qvalue"] < 0.01) & (psm_data_before["is_decoy"] == False)
+        ).sum()
+        id_psms_after = (
+            (psm_data_after["qvalue"] < 0.01) & (psm_data_after["is_decoy"] == False)
+        ).sum()
+        diff = id_psms_after - id_psms_before
+        diff_perc = diff / id_psms_before
+        logger.info(f"Identified {diff} ({diff_perc:.2%}) more PSMs at 1% FDR after rescoring.")
+
+        # Write output
+        logger.info(f"Writing output to {self.output_file_root}.psms.tsv...")
+        psm_utils.io.write_file(
+            psm_list,
+            self.output_file_root + ".psms.tsv",
+            filetype="tsv",
+            show_progressbar=True,
+        )
 
 
 def _match_psm_ids(old_id, regex_pattern):