Merge pull request #130 from wilhelm-lab/patch/0.7.2

Patch/0.7.2

.cookietemple.yml

@@ -15,5 +15,5 @@ full_name: Victor Giurcoiu
 email: victor.giurcoiu@tum.de
 project_name: spectrum_fundamentals
 project_short_description: Fundamentals public repo
-version: 0.7.1
+version: 0.7.2
 license: MIT

.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.7.1 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.7.1 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.7.2 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.7.2 # <<COOKIETEMPLE_FORCE_BUMP>>
 exclude-labels:
     - "skip-changelog"
 

cookietemple.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.7.1
+current_version = 0.7.2
 
 [bumpversion_files_whitelisted]
 init_file = spectrum_fundamentals/__init__.py

docs/conf.py

@@ -52,9 +52,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "0.7.1"
+version = "0.7.2"
 # The full version, including alpha/beta/rc tags.
-release = "0.7.1"
+release = "0.7.2"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "spectrum_fundamentals"
-version = "0.7.1"  # <<COOKIETEMPLE_FORCE_BUMP>>
+version = "0.7.2"  # <<COOKIETEMPLE_FORCE_BUMP>>
 description = "Fundamental functions, annotation pipeline and constants for oktoberfest"
 authors = ["Wilhelmlab at Technical University of Munich"]
 license = "MIT"

spectrum_fundamentals/__init__.py

@@ -2,7 +2,7 @@
 
 __author__ = "Mario Picciani"
 __email__ = "mario.picciani@tum.de"
-__version__ = "0.7.1"
+__version__ = "0.7.2"
 
 import logging
 import logging.handlers

spectrum_fundamentals/__main__.py

@@ -5,7 +5,7 @@
 
 
 @click.command()
-@click.version_option(version="0.7.1", message=click.style("spectrum_fundamentals Version: 0.7.1"))
+@click.version_option(version="0.7.2", message=click.style("spectrum_fundamentals Version: 0.7.2"))
 def main() -> None:
     """spectrum_fundamentals."""
 

spectrum_fundamentals/annotation/annotation.py

@@ -121,7 +121,7 @@ def annotate_spectra(
     un_annot_spectra: pd.DataFrame,
     mass_tolerance: Optional[float] = None,
     unit_mass_tolerance: Optional[str] = None,
-    custom_mods: Optional[Dict[str, Dict[str, Tuple[str, float]]]] = None,
+    custom_mods: Optional[Dict[str, float]] = None,
     fragmentation_method: str = "HCD",
 ) -> pd.DataFrame:
     """
@@ -142,7 +142,7 @@ def annotate_spectra(
     :param mass_tolerance: mass tolerance to calculate min and max mass
     :param unit_mass_tolerance: unit for the mass tolerance (da or ppm)
     :param fragmentation_method: fragmentation method that was used
-    :param custom_mods: Custom Modifications with the identifier, the unimod equivalent and the respective mass
+    :param custom_mods: mapping of custom UNIMOD string identifiers ('[UNIMOD:xyz]') to their mass
     :return: a Pandas DataFrame containing the annotated spectra with meta data
     """
     raw_file_annotations = []
@@ -345,7 +345,7 @@ def parallel_annotate(
     index_columns: Dict[str, int],
     mass_tolerance: Optional[float] = None,
     unit_mass_tolerance: Optional[str] = None,
-    custom_mods: Optional[Dict[str, Dict[str, Tuple[str, float]]]] = None,
+    custom_mods: Optional[Dict[str, float]] = None,
     fragmentation_method: str = "HCD",
 ) -> Optional[
     Union[
@@ -367,7 +367,7 @@ def parallel_annotate(
     :param index_columns: a dictionary that contains the index columns of the spectrum
     :param mass_tolerance: mass tolerance to calculate min and max mass
     :param unit_mass_tolerance: unit for the mass tolerance (da or ppm)
-    :param custom_mods: Custom Modifications with the identifier, the unimod equivalent and the respective mass
+    :param custom_mods: mapping of custom UNIMOD string identifiers ('[UNIMOD:xyz]') to their mass
     :param fragmentation_method: fragmentation method that was used
     :return: a tuple containing intensity values (np.ndarray), masses (np.ndarray), calculated mass (float),
              and any removed peaks (List[str])
@@ -397,7 +397,7 @@ def _annotate_linear_spectrum(
     index_columns: Dict[str, int],
     mass_tolerance: Optional[float],
     unit_mass_tolerance: Optional[str],
-    custom_mods: Optional[Dict[str, Dict[str, Tuple[str, float]]]] = None,
+    custom_mods: Optional[Dict[str, float]] = None,
     fragmentation_method: str = "HCD",
 ):
     """
@@ -407,7 +407,7 @@ def _annotate_linear_spectrum(
     :param index_columns: Index columns of the spectrum
     :param mass_tolerance: Mass tolerance for calculating min and max mass
     :param unit_mass_tolerance: Unit for the mass tolerance (da or ppm)
-    :param custom_mods: Custom Modifications with the identifier, the unimod equivalent and the respective mass
+    :param custom_mods: mapping of custom UNIMOD string identifiers ('[UNIMOD:xyz]') to their mass
     :param fragmentation_method: fragmentation method that was used
     :return: Annotated spectrum
     """
@@ -454,7 +454,7 @@ def _annotate_crosslinked_spectrum(
     crosslinker_type: str,
     mass_tolerance: Optional[float] = None,
     unit_mass_tolerance: Optional[str] = None,
-    custom_mods: Optional[Dict[str, Dict[str, Tuple[str, float]]]] = None,
+    custom_mods: Optional[Dict[str, float]] = None,
 ):
     """
     Annotate a crosslinked peptide spectrum.
@@ -464,7 +464,7 @@ def _annotate_crosslinked_spectrum(
     :param crosslinker_type: Type of crosslinker used
     :param mass_tolerance: Mass tolerance for calculating min and max mass
     :param unit_mass_tolerance: Unit for the mass tolerance (da or ppm)
-    :param custom_mods: Custom Modifications with the identifier, the unimod equivalent and the respective mass
+    :param custom_mods: mapping of custom UNIMOD string identifiers ('[UNIMOD:xyz]') to their mass
     :raises ValueError: if unsupported crosslinker type was supplied.
 
     :return: Annotated spectrum

spectrum_fundamentals/constants.py

@@ -1,5 +1,4 @@
 from enum import Enum
-from typing import Dict, List, Optional, Tuple
 
 import numpy as np
 
@@ -235,32 +234,6 @@
 }
 
 
-def update_mod_masses(mods: Optional[Dict[str, Dict[str, Tuple[str, float]]]] = None) -> Dict[str, float]:
-    """
-    Function to update MOD_MASSES with custom modifications.
-
-    :param mods: Modifications with respective mass
-    :raises AssertionError: if mass of modification was not provided as float.
-    :return: updated MOD_MASSES
-    """
-    mod_masses = {}
-    if mods:
-        try:
-            stat_mods: List[Tuple[str, float]] = [
-                (value[0], float(value[1])) for key, value in (mods.get("stat_mods") or {}).items()
-            ]
-            var_mods: List[Tuple[str, float]] = [
-                (value[0], float(value[1])) for key, value in (mods.get("var_mods") or {}).items()
-            ]
-        except ValueError as e:
-            raise AssertionError("All custom modifications value entries must be of type Tuple[str, float]") from e
-
-        for value in stat_mods + var_mods:
-            mod_masses[value[0]] = float(value[1])
-
-    return MOD_MASSES | mod_masses
-
-
 MOD_MASSES_SAGE = {
     "229.1629": "[UNIMOD:737]",
     "304.2071": "[UNIMOD:2016]",
@@ -276,6 +249,8 @@ def update_mod_masses(mods: Optional[Dict[str, Dict[str, Tuple[str, float]]]] =
     "42.0105": "[UNIMOD:1]",
 }
 # these are only used for prosit_grpc, oktoberfest uses the masses from MOD_MASSES
+
+
 AA_MOD_MASSES = {
     "K[UNIMOD:737]": AA_MASSES["K"] + MOD_MASSES["[UNIMOD:737]"],
     "M[UNIMOD:35]": AA_MASSES["M"] + MOD_MASSES["[UNIMOD:35]"],