check strand specificity in each drop group as opposed to all samples

drop/config/SampleAnnotation.py

@@ -48,10 +48,6 @@ def parse(self, sep='\t'):
 
         annotationTable = pd.read_csv(self.file, sep=sep, index_col=False)
 
-        # FRASER cannot handle a mixture of stranded and unstranded samples, raise error in such cases
-        if (annotationTable['STRAND'] == 'no').any() & ((annotationTable['STRAND'] == 'reverse').any() | (annotationTable['STRAND'] == 'yes').any()):
-            raise ValueError("Data contains a mix of stranded and unstranded samples. Please analyze them separately.\n")
-
         if annotationTable['STRAND'].isnull().values.any():
             raise ValueError("STRAND is not provided for some samples. All samples should have STRAND value in the sample annotation file.\n")
 

drop/config/submodules/AberrantSplicing.py

@@ -27,10 +27,11 @@ def __init__(self, config, sampleAnnotation, processedDataDir, processedResultsD
             if len(set(self.rnaIDs[g]) & set(self.rnaExIDs[g])) > 0:
                 raise ValueError(f"{set(self.rnaIDs[g]) & set(self.extRnaIDs[g])} has both BAM and external count file \
                 please fix in sample annotation table to only have either external count or BAM processing\n")
-
+   
         all_ids = self.sampleAnnotation.subsetGroups(self.groups, assay=["RNA", "SPLICE_COUNT"])
         self.checkSubset(all_ids)
-
+        self.checkStrandSpecificity()
+
     def setDefaultKeys(self, dict_):
         super().setDefaultKeys(dict_)
         setKey = utils.setKey
@@ -109,3 +110,15 @@ def getPsiTypeAssay(self):
         if(fraser_version == "FRASER2"):
             return "jaccard"
         return "theta"
+
+    def checkStrandSpecificity(self):
+        """
+        FRASER cannot handle a mixture of stranded and unstranded samples
+        raises an error in such cases
+        """
+
+        for drop_group in self.groups:
+            drop_group_annotation = self.sampleAnnotation.getIDsByGroup(drop_group)
+            drop_group_annotation = self.sampleAnnotation.subsetSampleAnnotation("RNA_ID", drop_group_annotation)
+            if (drop_group_annotation['STRAND'] == 'no').any() & ((drop_group_annotation['STRAND'] == 'reverse').any() | (drop_group_annotation['STRAND'] == 'yes').any()):
+                raise ValueError(f"Data contains a mix of stranded and unstranded samples in group: {drop_group}. Please analyze them separately.\n")