Merge pull request #69 from compomics/fix/xtandem-modifications

Fixes in `io.xtandem`

.vscode/settings.json

@@ -1,14 +1,13 @@
 {
-    "esbonio.sphinx.confDir": "${workspaceFolder}/docs/source",
-    "[python]": {
-        "editor.formatOnSave": true,
-        "editor.codeActionsOnSave": {"source.organizeImports": true},
-        "editor.rulers": [88]
+  "esbonio.sphinx.confDir": "${workspaceFolder}/docs/source",
+  "[python]": {
+    "editor.formatOnSave": true,
+    "editor.codeActionsOnSave": {
+      "source.organizeImports": "explicit"
     },
-    "python.formatting.provider": "black",
-    "python.testing.pytestArgs": [
-        "tests"
-    ],
-    "python.testing.unittestEnabled": false,
-    "python.testing.pytestEnabled": true
+    "editor.rulers": [99]
+  },
+  "python.testing.pytestArgs": ["tests"],
+  "python.testing.unittestEnabled": false,
+  "python.testing.pytestEnabled": true
 }

psm_utils/io/xtandem.py

@@ -55,7 +55,7 @@
 
 from psm_utils.exceptions import PSMUtilsException
 from psm_utils.io._base_classes import ReaderBase
-from psm_utils.peptidoform import Peptidoform
+from psm_utils.peptidoform import Peptidoform, format_number_as_string
 from psm_utils.psm import PSM
 
 logger = logging.getLogger(__name__)
@@ -119,34 +119,28 @@ def __iter__(self):
                 psm = self._parse_entry(entry, run)
                 yield psm
 
-    def _parse_peptidoform(self, peptide_entry, charge: int) -> Peptidoform:
-        """Parse X!Tandem XML peptide entry to :py:class:`~psm_utils.peptidoform.Peptidoform`."""
+    @staticmethod
+    def _parse_peptidoform(peptide_entry, charge):
         if "aa" in peptide_entry:
             # Parse modifications
             seq_list = list(peptide_entry["seq"])
-            mod_dict = {}
+            unmodified_seq = seq_list.copy()
+
             for mod_entry in peptide_entry["aa"]:
                 # Locations are encoded relative to position in protein
                 mod_loc = mod_entry["at"] - peptide_entry["start"]
+                mass_shift = float(mod_entry["modified"])
 
                 # Check if site matches amino acid
-                if not mod_entry["type"] == seq_list[mod_loc]:
+                if not mod_entry["type"] == unmodified_seq[mod_loc]:
                     raise XTandemModificationException(
                         f"Found unexpected residue `{seq_list[mod_loc]}` at "
                         f"modification location for `{mod_entry}`."
                     )
 
-                # Add modifications to dict
-                if mod_loc not in mod_dict:
-                    mod_dict[mod_loc] = float(mod_entry["modified"])
-                else:
-                    # "sum" multiple modifications per site, e.g.,
-                    # cmm + ammonia-loss = pyro-cmm
-                    mod_dict[mod_loc] += float(mod_entry["modified"])
-
-            # Add modification in ProForma format
-            for mod_loc, mass_shift in mod_dict.items():
-                seq_list[mod_loc] += f"[{mass_shift:+g}]"
+                # Add to sequence in ProForma format
+                seq_list[mod_loc] += f"[{format_number_as_string(mass_shift)}]"
+
             proforma_seq = "".join(seq_list)
 
         else:
@@ -170,7 +164,7 @@ def _parse_entry(self, entry, run: str) -> PSM:
             precursor_mz=entry["mh"] - mass.nist_mass["H"][0][0],
             retention_time=entry["rt"],
             run=run,
-            protein_list=[entry["protein"][0]["label"]],
+            protein_list=[protein["label"] for protein in entry["protein"]],
             source="X!Tandem",
             provenance_data={
                 "xtandem_filename": str(self.filename),

psm_utils/peptidoform.py

@@ -407,7 +407,7 @@ def _rename_modification_list(mods):
             for mod in mods:
                 try:
                     if isinstance(mod, proforma.MassModification):
-                        mod_value = _format_number_as_string(mod.value)
+                        mod_value = format_number_as_string(mod.value)
                     else:
                         mod_value = mod.value
                     if mod_value in mapping:
@@ -517,14 +517,16 @@ def apply_fixed_modifications(self):
             self.properties["fixed_modifications"] = []
 
 
-def _format_number_as_string(num):
+def format_number_as_string(num):
     """Format number as string for ProForma mass modifications."""
     # Using this method over `:+g` string formatting to avoid rounding and scientific notation
+    num = float(num)
     plus = "+" if np.sign(num) == 1 else ""  # Add plus sign if positive
     num = str(num).rstrip("0").rstrip(".")  # Remove trailing zeros and decimal point
     return plus + num
 
 
+
 class PeptidoformException(PSMUtilsException):
     """Error while handling :py:class:`Peptidoform`."""
 

tests/test_io/test_xtandem.py

@@ -35,7 +35,7 @@ def test__parse_peptidoform(self):
                     },
                     2,
                 ),
-                "expected_out": "C[+39.9954]WASLWTAR/2",
+                "expected_out": "C[+57.022][-17.02655]WASLWTAR/2",
             },
         ]
 

tests/test_peptidoform.py

@@ -1,6 +1,6 @@
 from pyteomics import proforma
 
-from psm_utils.peptidoform import Peptidoform, _format_number_as_string
+from psm_utils.peptidoform import Peptidoform, format_number_as_string
 
 
 class TestPeptidoform:
@@ -63,4 +63,4 @@ def test_format_number_as_string():
     ]
 
     for test_case_in, expected_out in test_cases:
-        assert _format_number_as_string(test_case_in) == expected_out
+        assert format_number_as_string(test_case_in) == expected_out