Merge pull request #403 from zargham-ahmad/matchms-formatter

Improved formatter.py performance
RECETOX · Sep 27, 2023 · 1cacfa4 · 1cacfa4
2 parents b0e7b33 + 0ab3112
commit 1cacfa4
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/tools/matchms/formatter.py b/tools/matchms/formatter.py
@@ -13,10 +13,12 @@ def scores_to_dataframe(scores):
         DataFrame: Scores
         DataFrame: Matches
     """
-    dataframe = DataFrame(columns=['query', 'reference', *scores.scores.score_names])
+    data = []
 
     for i, (row, col) in enumerate(zip(scores.scores.row, scores.scores.col)):
-        dataframe.loc[i] = [scores.queries[col].metadata['compound_name'], scores.references[row].metadata['compound_name'], *scores.scores.data[i]]
+        data.append([scores.queries[col].metadata['compound_name'], scores.references[row].metadata['compound_name'], *scores.scores.data[i]])
+
+    dataframe = DataFrame(data, columns=['query', 'reference', *scores.scores.score_names])
 
     return dataframe
 

diff --git a/tools/matchms/matchms_formatter.xml b/tools/matchms/matchms_formatter.xml
@@ -1,4 +1,4 @@
-<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy1" profile="21.09">
+<tool id="matchms_formatter" name="matchms scores formatter" version="@TOOL_VERSION@+galaxy2" profile="21.09">
     <description>reformat scores object of matchms to long format table</description>
 
     <macros>