Bugfix atomic isotopes

compomics · Jun 23, 2023 · 4d46071 · 4d46071
1 parent e7e6ca3
commit 4d46071
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Showing 3 changed files with 24 additions and 6 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+# [2.2.2] - 2023-06-23
+
+### Changed
+- Fixed a bug where isotopes are incorrectly parsed
+
 # [2.2.1] - 2023-06-18
 
 ### Changed

diff --git a/deeplc/feat_extractor.py b/deeplc/feat_extractor.py
@@ -546,11 +546,24 @@ def rolling_sum(a, n=2):
                         continue
 
                     for atom_position_composition,atom_change in modification_composition.items():
-                        matrix[i, dict_index[atom_position_composition]] += atom_change
-                        if i in positions:
-                            matrix_pos[i, dict_index_pos[atom_position_composition]] += atom_change
-                        elif i - seq_len in positions:
-                            matrix_pos[i - seq_len, dict_index_pos[atom_position_composition]] += atom_change
+                        try:
+                            matrix[i, dict_index[atom_position_composition]] += atom_change
+                            if i in positions:
+                                matrix_pos[i, dict_index_pos[atom_position_composition]] += atom_change
+                            elif i - seq_len in positions:
+                                matrix_pos[i - seq_len, dict_index_pos[atom_position_composition]] += atom_change
+                        except KeyError:
+                            try:
+                                logger.debug(f"Could not add the following atom: {atom_position_composition}, attempting to replace the [] part")
+                                atom_position_composition = sub("\[.*?\]", "", atom_position_composition)
+                                matrix[i, dict_index[atom_position_composition]] += atom_change
+                                if i in positions:
+                                    matrix_pos[i, dict_index_pos[atom_position_composition]] += atom_change
+                                elif i - seq_len in positions:
+                                    matrix_pos[i - seq_len, dict_index_pos[atom_position_composition]] += atom_change
+                            except KeyError:
+                                logger.debug(f"Could not add the following atom: {atom_position_composition}, second attempt, now ignored")
+                                continue
 
             #logger.debug(
             #    "Peptide onehot+mod: %s seconds" %

diff --git a/setup.py b/setup.py
@@ -6,7 +6,7 @@
 
 setup(
     name='deeplc',
-    version='2.2.1',
+    version='2.2.2',
     license='apache-2.0',
     description='DeepLC: Retention time prediction for (modified) peptides using Deep Learning.',
     long_description=LONG_DESCRIPTION,