added column to feature metadata retaining RT in seconds

phenomecentre · Dec 6, 2023 · 0c8fed7 · 0c8fed7
1 parent ef4134e
commit 0c8fed7
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/Tests/test_coverage.sh b/Tests/test_coverage.sh
@@ -4,7 +4,7 @@
 
 coverage erase
 coverage run -m unittest discover
-coverage report
+coverage report --sort=Cover
 coverage html
-coverage xml
+#coverage xml
 open htmlcov/index.html
diff --git a/nPYc/objects/_msDataset.py b/nPYc/objects/_msDataset.py
@@ -867,7 +867,9 @@ def _loadXCMSDataset(self, path, noFeatureParams=14):
 		# Tidy formatting
 		featureMetadata.drop(list(featureMetadata.filter(regex='Unnamed')), axis=1, inplace=True)
 		featureMetadata.rename(columns={"name": "Feature Name", "mz": "m/z", "rt": "Retention Time"}, inplace=True)
-		featureMetadata['Retention Time'] = featureMetadata['Retention Time'].astype(float) / 60.0
+		# Jazz adding extra column to retain RT in seconds as well as minutes
+		featureMetadata['Retention Time (seconds)'] = featureMetadata['Retention Time'].astype(float)
+		featureMetadata['Retention Time'] = featureMetadata['Retention Time (seconds)'] / 60.0
 		featureMetadata['m/z'] = featureMetadata['m/z'].astype(float)
 
 		self.featureMetadata = featureMetadata