Add support for adding and applying global terminal modifications.

For now using a workaround while waiting for official support and an implementation in Pyteomics. See HUPO-PSI/ProForma#6
compomics · Mar 18, 2024 · 0297b77 · 0297b77
1 parent 56ed71d
commit 0297b77
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Showing 2 changed files with 35 additions and 8 deletions.
diff --git a/psm_utils/peptidoform.py b/psm_utils/peptidoform.py
@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+from collections import defaultdict
 from typing import Iterable, List, Tuple, Union
 
 import numpy as np
@@ -14,7 +15,7 @@ class Peptidoform:
     Peptide sequence, modifications and charge state represented in ProForma notation.
     """
 
-    def __init__(self, proforma_sequence: [str, proforma.ProForma]) -> None:
+    def __init__(self, proforma_sequence: Union[str, proforma.ProForma]) -> None:
         """
         Peptide sequence, modifications and charge state represented in ProForma notation.
 
@@ -454,7 +455,7 @@ def add_fixed_modifications(
 
         See also
         --------
-        psm_utils.peptidoform.Peptidoform.add_fixed_modifications
+        psm_utils.peptidoform.Peptidoform.apply_fixed_modifications
 
         Examples
         --------
@@ -463,6 +464,14 @@ def add_fixed_modifications(
         >>> peptidoform.proforma
         '<[Carbamidomethyl]@C>ATPEILTCNSIGCLK'
 
+        Notes
+        -----
+        While globally defined terminal modifications are not explicitly supported in ProForma v2,
+        this function supports adding terminal modifications using the ``N-term`` and ``C-term``
+        targets in place of an amino acid target. These global modifications are supported in the
+        :py:meth:`psm_utils.peptidoform.Peptidoform.apply_fixed_modifications` method through a
+        workaround. See https://github.com/HUPO-PSI/ProForma/issues/6 for discussions on the issue.
+
         """
         if isinstance(modification_rules, dict):
             modification_rules = modification_rules.items()
@@ -497,13 +506,10 @@ def apply_fixed_modifications(self):
         """
         if self.properties["fixed_modifications"]:
             # Setup target_aa -> modification_list dictionary
-            rule_dict = {}
+            rule_dict = defaultdict(list)
             for rule in self.properties["fixed_modifications"]:
                 for target_aa in rule.targets:
-                    try:
-                        rule_dict[target_aa].append(rule.modification_tag)
-                    except KeyError:
-                        rule_dict[target_aa] = [rule.modification_tag]
+                    rule_dict[target_aa].append(rule.modification_tag)
 
             # Apply modifications to sequence
             for i, (aa, site_mods) in enumerate(self.parsed_sequence):
@@ -513,6 +519,14 @@ def apply_fixed_modifications(self):
                     else:
                         self.parsed_sequence[i] = (aa, rule_dict[aa])
 
+            # Apply terminal modifications
+            for term, term_name in [("n_term", "N-term"), ("c_term", "C-term")]:
+                if term_name in rule_dict:
+                    if self.properties[term]:
+                        self.properties[term].extend(rule_dict[term_name])
+                    else:
+                        self.properties[term] = rule_dict[term_name]
+
             # Remove fixed modifications
             self.properties["fixed_modifications"] = []
 
@@ -526,7 +540,6 @@ def format_number_as_string(num):
     return plus + num
 
 
-
 class PeptidoformException(PSMUtilsException):
     """Error while handling :py:class:`Peptidoform`."""
 

diff --git a/tests/test_peptidoform.py b/tests/test_peptidoform.py
@@ -51,6 +51,20 @@ def test_rename_modifications(self):
             peptidoform.rename_modifications(label_mapping)
             assert peptidoform.proforma == expected_out
 
+    def test_add_apply_fixed_modifications(self):
+        test_cases = [
+            ("ACDEK", [("Cmm", ["C"])], "AC[Cmm]DEK"),
+            ("AC[Cmm]DEK", [("SecondMod", ["C"])], "AC[Cmm][SecondMod]DEK"),
+            ("ACDEK", [("TMT6plex", ["K", "N-term"])], "[TMT6plex]-ACDEK[TMT6plex]"),
+            ("ACDEK-[CT]", [("TMT6plex", ["K", "N-term"])], "[TMT6plex]-ACDEK[TMT6plex]-[CT]"),
+        ]
+
+        for test_case_in, fixed_modifications, expected_out in test_cases:
+            peptidoform = Peptidoform(test_case_in)
+            peptidoform.add_fixed_modifications(fixed_modifications)
+            peptidoform.apply_fixed_modifications()
+            assert peptidoform.proforma == expected_out
+
 
 def test_format_number_as_string():
     test_cases = [