refine logic of terminal feature selection

BojarLab · Jun 28, 2024 · db9e9f9 · db9e9f9
1 parent 3098e80
commit db9e9f9
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Showing 6 changed files with 8 additions and 8 deletions.
diff --git a/build/lib/glycowork/motif/analysis.py b/build/lib/glycowork/motif/analysis.py
@@ -1511,7 +1511,7 @@ def get_glycoshift_per_site(df, group1, group2, paired = False, impute = True,
   df, df_org, group1, group2 = preprocess_data(df, group1, group2, experiment = "diff", motifs = False, impute = impute,
                                                min_samples = min_samples, transform = "Nothing", paired = paired)
   alpha = get_alphaN(len(group1+group2))
-  df, glycan_features = process_for_glycoshift(df) # potentially expand this further to infer and label high-Man/Hybrid/complex
+  df, glycan_features = process_for_glycoshift(df)
   necessary_columns = ['Glycoform'] + glycan_features
   preserved_data = df[necessary_columns]
   df = df.drop(necessary_columns, axis = 1)

diff --git a/build/lib/glycowork/motif/annotate.py b/build/lib/glycowork/motif/annotate.py
@@ -234,9 +234,9 @@ def annotate_switchboard(glycan):
     shopping_cart.append(temp)
   if 'chemical' in feature_set:
     shopping_cart.append(get_molecular_properties(glycans, placeholder = True))
-  if 'terminal' or 'terminal1' or 'terminal2' in feature_set:
+  if 'terminal' in feature_set or 'terminal1' in feature_set or 'terminal2' in feature_set:
     bag1, bag2 = [], []
-    if 'terminal' or 'terminal1' in feature_set:
+    if 'terminal' in feature_set or 'terminal1' in feature_set:
       bag1 = list(map(get_terminal_structures, glycans))
     if 'terminal2' in feature_set:
       bag2 = [get_terminal_structures(glycan, size = 2) for glycan in glycans]

diff --git a/build/lib/glycowork/motif/processing.py b/build/lib/glycowork/motif/processing.py
@@ -987,7 +987,7 @@ def infer_features_from_composition(comp):
     feature_dic['high_Man'] = 1
   else:
     feature_dic['high_Man'] = 0
-  if (comp.get('A', 0) + comp.get('G', 0) < 2 and comp.get('H', 0) > 4) or (comp.get('Neu5Ac', 0) + comp.get('Neu5Gc', 0) > 1 and comp.get('Hex', 0) > 4):
+  if (comp.get('A', 0) + comp.get('G', 0) < 2 and comp.get('H', 0) > 4) or (comp.get('Neu5Ac', 0) + comp.get('Neu5Gc', 0) < 2 and comp.get('Hex', 0) > 4):
     feature_dic['hybrid'] = 1
   else:
     feature_dic['hybrid'] = 0

diff --git a/glycowork/motif/analysis.py b/glycowork/motif/analysis.py
@@ -1511,7 +1511,7 @@ def get_glycoshift_per_site(df, group1, group2, paired = False, impute = True,
   df, df_org, group1, group2 = preprocess_data(df, group1, group2, experiment = "diff", motifs = False, impute = impute,
                                                min_samples = min_samples, transform = "Nothing", paired = paired)
   alpha = get_alphaN(len(group1+group2))
-  df, glycan_features = process_for_glycoshift(df) # potentially expand this further to infer and label high-Man/Hybrid/complex
+  df, glycan_features = process_for_glycoshift(df)
   necessary_columns = ['Glycoform'] + glycan_features
   preserved_data = df[necessary_columns]
   df = df.drop(necessary_columns, axis = 1)

diff --git a/glycowork/motif/annotate.py b/glycowork/motif/annotate.py
@@ -234,9 +234,9 @@ def annotate_switchboard(glycan):
     shopping_cart.append(temp)
   if 'chemical' in feature_set:
     shopping_cart.append(get_molecular_properties(glycans, placeholder = True))
-  if 'terminal' or 'terminal1' or 'terminal2' in feature_set:
+  if 'terminal' in feature_set or 'terminal1' in feature_set or 'terminal2' in feature_set:
     bag1, bag2 = [], []
-    if 'terminal' or 'terminal1' in feature_set:
+    if 'terminal' in feature_set or 'terminal1' in feature_set:
       bag1 = list(map(get_terminal_structures, glycans))
     if 'terminal2' in feature_set:
       bag2 = [get_terminal_structures(glycan, size = 2) for glycan in glycans]

diff --git a/glycowork/motif/processing.py b/glycowork/motif/processing.py
@@ -987,7 +987,7 @@ def infer_features_from_composition(comp):
     feature_dic['high_Man'] = 1
   else:
     feature_dic['high_Man'] = 0
-  if (comp.get('A', 0) + comp.get('G', 0) < 2 and comp.get('H', 0) > 4) or (comp.get('Neu5Ac', 0) + comp.get('Neu5Gc', 0) > 1 and comp.get('Hex', 0) > 4):
+  if (comp.get('A', 0) + comp.get('G', 0) < 2 and comp.get('H', 0) > 4) or (comp.get('Neu5Ac', 0) + comp.get('Neu5Gc', 0) < 2 and comp.get('Hex', 0) > 4):
     feature_dic['hybrid'] = 1
   else:
     feature_dic['hybrid'] = 0