Update validateData.py

Fixed an error in naming alleles for the mutation file checks in SNP, DNP, and TNP. (tumor_seq_allele1 was repeated twice, instead of tumor_seq_allele2)
cBioPortal · Aug 10, 2023 · 47968c9 · 47968c9
1 parent 7b2bbe2
commit 47968c9
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/core/src/main/scripts/importer/validateData.py b/core/src/main/scripts/importer/validateData.py
@@ -1928,23 +1928,23 @@ def checkAlleleMAFFormat(self, data):
 
             if variant_type == "SNP":
                 # Expect alleles to have length 2 when variant type is SNP
-                if not (len(ref_allele) == 1 and len(tumor_seq_allele1) == 1 and len(tumor_seq_allele1) == 1):
+                if not (len(ref_allele) == 1 and len(tumor_seq_allele1) == 1 and len(tumor_seq_allele2) == 1):
                     log_message = "Variant_Type indicates a SNP, but length of Reference_Allele, Tumor_Seq_Allele1 " \
                                   "and/or Tumor_Seq_Allele2 do not equal 1."
                     extra_dict = {'line_number': self.line_number,
                                   'cause': '(%s, %s, %s)' % (ref_allele, tumor_seq_allele1, tumor_seq_allele2)}
                     self.send_log_message(self.strict_maf_checks, log_message, extra_dict)
             if variant_type == "DNP":
                 # Expect alleles to have length 2 when variant type is DNP
-                if not (len(ref_allele) == 2 and len(tumor_seq_allele1) == 2 and len(tumor_seq_allele1) == 2):
+                if not (len(ref_allele) == 2 and len(tumor_seq_allele1) == 2 and len(tumor_seq_allele2) == 2):
                     log_message = "Variant_Type indicates a DNP, but length of Reference_Allele, Tumor_Seq_Allele1 " \
                                   "and/or Tumor_Seq_Allele2 do not equal 2."
                     extra_dict = {'line_number': self.line_number,
                                   'cause': '(%s, %s, %s)' % (ref_allele, tumor_seq_allele1, tumor_seq_allele2)}
                     self.send_log_message(self.strict_maf_checks, log_message, extra_dict)
             if variant_type == "TNP":
                 # Expect alleles to have length 3 when variant type is TNP
-                if not (len(ref_allele) == 3 and len(tumor_seq_allele1) == 3 and len(tumor_seq_allele1) == 3):
+                if not (len(ref_allele) == 3 and len(tumor_seq_allele1) == 3 and len(tumor_seq_allele2) == 3):
                     log_message = "Variant_Type indicates a TNP, but length of Reference_Allele, Tumor_Seq_Allele1 " \
                                   "and/or Tumor_Seq_Allele2 do not equal 3."
                     extra_dict = {'line_number': self.line_number,