Fix number of columns in SV tsv data file

cBioPortal · Jun 4, 2024 · d7e8ff3 · d7e8ff3
1 parent 0cdda9d
commit d7e8ff3
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/tests/test_data/study_es_0_inc/data_structural_variants.txt b/tests/test_data/study_es_0_inc/data_structural_variants.txt
@@ -1,10 +1,10 @@
 Sample_Id	Site1_Entrez_Gene_Id	Site1_Hugo_Symbol	Site1_Ensembl_Transcript_Id	Site1_Region_Number	Site1_Chromosome	Site1_Position	Site1_Region	Site1_Description	Site2_Entrez_Gene_Id	Site2_Hugo_Symbol	Site2_Ensembl_Transcript_Id	Site2_Region_Number	Site2_Chromosome	Site2_Position	Site2_Contig	Site2_Region	Site2_Description	Site2_Effect_On_Frame	NCBI_Build	DNA_Support	RNA_Support	Normal_Read_Count	Tumor_Read_Count	Normal_Variant_Count	Tumor_Variant_Count	Normal_Paired_End_Read_Count	Tumor_Paired_End_Read_Count	Normal_Split_Read_Count	Tumor_Split_Read_Count	Annotation	Breakpoint_Type	Center	Connection_Type	Event_Info	Class	SV_Length	Comments	External_Annotation	cbp_driver	cbp_driver_annotation	cbp_driver_tiers	cbp_driver_tiers_annotation	SV_Status	StructVarNs.column1	StructVarNs2.lorem	StructVarNs.column2
 TCGA-BH-NEW	NA	PIEZO1	ENST00000242365	15	7	138536968	EXON	PIEZO1-NCOA4.K16B10.COSF509_1	NA	NCOA4	ENST00000288602	10	7	140482957		EXON	PIEZO1-NCOA4.PIEZO1.COSF509_2	NA	GRCh37	no	yes	NA	1000	NA	900	NA	NA	NA	NA	PIEZO1-NCOA4.K16B10.COSF509	NA	NA	NA	Fusion	NA	NA	Gain-of-Function	COSMIC:COSF509	Putative_Driver	Test driver Foo	Class 4	Class annotation	SOMATIC	value1	ipsum	value2
 TCGA-BH-NEW	NA	KIAA1549	ENST00000242365	15	7	138536968	EXON	KIAA1549-BRAF.K16B10.COSF509_1	NA	BRAF	ENST00000288602	10	7	140482957		EXON	KIAA1549-BRAF.K16B10.COSF509_2	NA	GRCh37	no	yes	NA	1000	NA	900	NA	NA	NA	NA	KIAA1549-BRAF.K16B10.COSF509	NA	NA	NA	Fusion	NA	NA	Gain-of-Function	COSMIC:COSF509	Putative_Driver	Test driver	Class 4	Class annotation	SOMATIC	value1	ipsum	value2
-TCGA-A1-A0SB-03	NA	NCOA4	ENST00000344348	7	10	51582939	EXON	NCOA4-RET.N7R12_1	NA	RET	ENST00000340058	12	10	43612031		EXON	NCOA4-RET.N7R12_2	NA	GRCh37	no	yes	NA	1001	NA	800	NA	NA	NA	NA	NCOA4-RET.N7R1	NA	NA	NA	Fusion	NA	NA	Gain-of-Function	NA	Putative_Passenger	Test driver	Class 3	Class annotation	SOMATIC
+TCGA-A1-A0SB-03	NA	NCOA4	ENST00000344348	7	10	51582939	EXON	NCOA4-RET.N7R12_1	NA	RET	ENST00000340058	12	10	43612031		EXON	NCOA4-RET.N7R12_2	NA	GRCh37	no	yes	NA	1001	NA	800	NA	NA	NA	NA	NCOA4-RET.N7R1	NA	NA	NA	Fusion	NA	NA	Gain-of-Function	NA	Putative_Passenger	Test driver	Class 3	Class annotation	SOMATIC			
 TCGA-BH-NEW	NA	EML4	ENST00000318522	6	2	42492091	EXON	EML4-ALK.E6bA20.AB374362_1	NA	ALK	ENST00000389048	20	2	29446394		EXON	EML4-ALK.E6bA20.AB374362_2	NA	GRCh37	no	yes	NA	1002	NA	700	NA	NA	NA	NA	EML4-ALK.E6bA20.AB374362	NA	NA	NA	Fusion	NA	NA	Gain-of-Function	GENBANK:AB374362	Putative_Driver	Test driver	Class 2	Class annotation	SOMATIC			
 TCGA-BH-NEW	NA	TMPRSS2	ENST00000332149	1	21	42880007	EXON	TMPRSS2-ERG.T1E2.COSF23.1_1	NA	ERG	ENST00000442448	2	21	39956869		EXON	TMPRSS2-ERG.T1E2.COSF23.1_2	NA	GRCh37	no	yes	NA	1003	NA	600	NA	NA	NA	NA	TMPRSS2-ERG.T1E2.COSF23.1	NA	NA	NA	Fusion	NA	NA	Gain-of-Function	COSMIC:COSF23	Unknown	Test driver	Class 1	Class annotation	SOMATIC			
-TCGA-A1-A0SB-01	NA	EGFR	ENST00000275493	1	7	55087058	EXON	EGFR-EGFR.E1E8.DelPositive.1_1	NA	EGFR	ENST00000275493	8	7	55223522		EXON	EGFR-EGFR.E1E8.DelPositive.1_2	NA	GRCh37	no	yes	NA	1004	NA	500	NA	NA	NA	NA	EGFR-EGFR.E1E8.DelPositive	NA	NA	NA	Fusion	NA	NA	NA	NA	Putative_Driver	Test driver	Unknown	Class annotation	SOMATIC
+TCGA-A1-A0SB-01	NA	EGFR	ENST00000275493	1	7	55087058	EXON	EGFR-EGFR.E1E8.DelPositive.1_1	NA	EGFR	ENST00000275493	8	7	55223522		EXON	EGFR-EGFR.E1E8.DelPositive.1_2	NA	GRCh37	no	yes	NA	1004	NA	500	NA	NA	NA	NA	EGFR-EGFR.E1E8.DelPositive	NA	NA	NA	Fusion	NA	NA	NA	NA	Putative_Driver	Test driver	Unknown	Class annotation	SOMATIC			
 TCGA-BH-NEW	NA	ALK	ENST00000389048	11	2	29497964	EXON	ALK-PTPN3.A11P3_1	NA	PTPN3	ENST00000374541	3	9	112219679		EXON	ALK-PTPN3.A11P3_2	NA	GRCh37	no	yes	NA	1005	NA	400	NA	NA	NA	NA	ALK-PTPN3.A11P3	NA	NA	NA	Fusion	NA	NA	NA	NA	NA	NA	NA	NA	SOMATIC			
 TCGA-A1-A0SB-01	NA	EML4	ENST00000318522	13	2	42522656	EXON	EML4-ALK.E13A20.AB462411_1	NA	ALK	ENST00000389048	20	2	29446335		EXON	EML4-ALK.E13A20.AB462411_2	NA	GRCh37	no	yes	NA	1006	NA	300	NA	NA	NA	NA	EML4-ALK.E13A20	NA	NA	NA	Fusion	NA	NA	Gain-of-Function	GENBANK:AB462411	NA	NA	NA	NA	SOMATIC			
 TCGA-A1-A0SB-03	NA	TMPRSS2	ENST00000455813	1	21	42870045	EXON	TMPRSS2-ETV1.T1bE4_1	NA	ETV1	ENST00000405358	4	7	14017105		EXON	TMPRSS2-ETV1.T1bE4_2	NA	GRCh37	no	yes	NA	1007	NA	200	NA	NA	NA	NA	TMPRSS2-ETV1.T1bE4	NA	NA	NA	Fusion	NA	NA	NA	NA	NA	NA	NA	NA	SOMATIC