New backup 2025-03-04 10:10:44

examples/rtd_tutorial.py

@@ -821,12 +821,12 @@
 clf_out = methyl_analysis.classify(ids=ids, clf_list="none-kbest-rf")
 
 ## Output accuracy scores:
-print("Accuracy Scores:", clf_out.metrics["accuracy_scores"])
+print("Accuracy Scores:", clf_out[0].metrics["accuracy_scores"])
 """
 Accuracy Scores: [1.0, 1.0, 1.0, 1.0, 1.0]
 """
 ## Detailed classifier report of first sample:
-print(clf_out.reports[0])
+print(clf_out[0].reports[0])
 """
 201530470054_R05C01
 ===================
@@ -859,6 +859,7 @@
 # Perform prediction on beta values:
 
 ## Number of CpGs in the dataset
+methyl_analysis.set_betas()
 n_cpgs = methyl_analysis.betas_all.shape[1]
 ## Generate random beta values for 10 artificial samples
 random_beta_values = pd.DataFrame(
@@ -909,7 +910,7 @@
 ids = methyl_analysis.idat_handler.ids
 clf_out = methyl_analysis.classify(ids=ids, clf_list=rf_clf)
 
-print(clf_out.reports[0])
+print(clf_out[0].reports[0])
 """
 201530470054_R05C01
 ===================
@@ -949,7 +950,7 @@
 ids = methyl_analysis.idat_handler.ids
 clf_out = methyl_analysis.classify(ids=ids, clf_list=et_clf)
 
-print(clf_out.reports[0])
+print(clf_out[0].reports[0])
 """
 201530470054_R05C01
 ===================
@@ -1000,7 +1001,7 @@ def predict_proba(self, betas, id_=None):
     def classes(self):
         return self._classes
 
-    def info(self):
+    def info(self, output_format="txt"):
         return "This text will be printed in reports."
 
     def metrics(self):
@@ -1013,7 +1014,7 @@ def metrics(self):
 ## Perform classification
 clf_out = methyl_analysis.classify(ids=ids, clf_list=custom_clf)
 
-print(clf_out.reports[0])
+print(clf_out[0].reports[0])
 """
 201530470054_R05C01
 ===================

mepylome/analysis/methyl.py

@@ -1789,7 +1789,7 @@ def classify(
         Raises:
             ValueError: If not exactly one if `ids` or `values` is set.
         """
-        if sum(bool(x) for x in (ids, values)) != 1:
+        if sum(x is not None for x in (ids, values)) != 1:
             msg = "Provide exactly one of 'ids' or 'values'."
             raise ValueError(msg)