From 47968c9c43f398813e341f61ec97c58cc34cf1a7 Mon Sep 17 00:00:00 2001 From: Sowmiyaa Kumar <109506589+sowmiyaa-kumar@users.noreply.github.com> Date: Tue, 20 Jun 2023 19:01:17 +0200 Subject: [PATCH] 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) --- core/src/main/scripts/importer/validateData.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/core/src/main/scripts/importer/validateData.py b/core/src/main/scripts/importer/validateData.py index 28d2d07b429..e6cf2c63f7b 100755 --- a/core/src/main/scripts/importer/validateData.py +++ b/core/src/main/scripts/importer/validateData.py @@ -1928,7 +1928,7 @@ 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, @@ -1936,7 +1936,7 @@ def checkAlleleMAFFormat(self, data): 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, @@ -1944,7 +1944,7 @@ def checkAlleleMAFFormat(self, data): 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,