support glycan graphs as input in get_match

BojarLab · Mar 11, 2024 · 893e3cc · 893e3cc
1 parent a29925b
commit 893e3cc
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Showing 3 changed files with 7 additions and 9 deletions.
diff --git a/build/lib/glycowork/motif/annotate.py b/build/lib/glycowork/motif/annotate.py
@@ -76,10 +76,7 @@ def annotate_glycan(glycan, motifs = None, termini_list = [], gmotifs = None):
   out = pd.DataFrame(columns = motifs.motif_name if isinstance(motifs, pd.DataFrame) else motifs)
   out.loc[0] = res
   out.loc[0] = out.loc[0].astype('int')
-  if isinstance(glycan, str):
-    out.index = [glycan]
-  else:
-    out.index = [graph_to_string(glycan)]
+  out.index = [glycan] if isinstance(glycan, str) else [graph_to_string(glycan)]
   return out
 
 

diff --git a/glycowork/motif/annotate.py b/glycowork/motif/annotate.py
@@ -76,10 +76,7 @@ def annotate_glycan(glycan, motifs = None, termini_list = [], gmotifs = None):
   out = pd.DataFrame(columns = motifs.motif_name if isinstance(motifs, pd.DataFrame) else motifs)
   out.loc[0] = res
   out.loc[0] = out.loc[0].astype('int')
-  if isinstance(glycan, str):
-    out.index = [glycan]
-  else:
-    out.index = [graph_to_string(glycan)]
+  out.index = [glycan] if isinstance(glycan, str) else [graph_to_string(glycan)]
   return out
 
 

diff --git a/glycowork/motif/regex.py b/glycowork/motif/regex.py
@@ -621,7 +621,11 @@ def get_match(pattern, glycan, return_matches = True):
   lookahead_snuck_in = False
   if any([k in glycan for k in [';', '-D-', 'RES', '=']]):
     glycan = canonicalize_iupac(glycan)
-  ggraph = glycan_to_nxGraph(glycan)
+  if isinstance(glycan, str):
+    ggraph = glycan_to_nxGraph(glycan)
+  else:
+    ggraph = glycan
+    glycan = graph_to_string(ggraph)
   pattern_components = preprocess_pattern(pattern) if isinstance(pattern, str) else pattern
   pattern_matches = match_it_up(pattern_components, glycan, ggraph)
   if pattern_matches: