Add support for sign missing in proforma string

wfondrie · May 8, 2024 · e603993 · e603993
1 parent 8519369
commit e603993
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Showing 2 changed files with 13 additions and 2 deletions.
diff --git a/depthcharge/primitives.py b/depthcharge/primitives.py
@@ -73,7 +73,12 @@ def __post_init__(self) -> None:
                 continue
 
             try:
-                mod = [MassModification(mod)]
+                try:
+                    mass = mod[0].value
+                except (IndexError, AttributeError):
+                    mass = mod
+
+                mod = [MassModification(float(mass))]
             except ValueError:
                 try:
                     mod = [GenericModification(mod)]
@@ -116,7 +121,7 @@ def split(self) -> list[str]:
                 except (AttributeError, ValueError):
                     modstr = f"[{mods[0].mass:+0.6f}]"
             else:
-                modstr = f"[{sum([m.mass for m in mods]):+0.6f}]"
+                modstr = f"[{sum(m.mass for m in mods):+0.6f}]"
 
             if not idx:
                 out.append(f"{modstr}-")

diff --git a/tests/unit_tests/test_primitives.py b/tests/unit_tests/test_primitives.py
@@ -50,6 +50,12 @@ def test_peptide_init():
     assert parsed.split() == expected
 
 
+def test_almost_proforma():
+    """Test a peptide lacking an explicit sign."""
+    parsed = Peptide.from_proforma("LES[79.0]LIEK")
+    assert parsed.split() == ["L", "E", "S[79.000000]", "L", "I", "E", "K"]
+
+
 def test_peptide_from_proforma():
     """Test proforma parsing."""
     parsed = Peptide.from_proforma("LESLIEK/2")