Test for running fusion file in the pipeline

griffithlab · Jan 17, 2017 · 16ce34f · 16ce34f
1 parent c54aacf
commit 16ce34f
Show file tree

Hide file tree

Showing 14 changed files with 5,341 additions and 4,726 deletions.
diff --git a/tests/test_data/pvacseq/MHC_Class_I/tmp/Test.HLA-G*01:09.10.parsed.tsv_1-48 b/tests/test_data/pvacseq/MHC_Class_I/tmp/Test.HLA-G*01:09.10.parsed.tsv_1-48
diff --git a/tests/test_data/pvacseq/MHC_Class_I/tmp/Test.HLA-G*01:09.9.parsed.tsv_1-48 b/tests/test_data/pvacseq/MHC_Class_I/tmp/Test.HLA-G*01:09.9.parsed.tsv_1-48
diff --git a/tests/test_data/pvacseq/fusions/MHC_Class_I/Test.combined.parsed.tsv b/tests/test_data/pvacseq/fusions/MHC_Class_I/Test.combined.parsed.tsv
diff --git a/tests/test_data/pvacseq/fusions/MHC_Class_I/Test.filtered.binding.tsv b/tests/test_data/pvacseq/fusions/MHC_Class_I/Test.filtered.binding.tsv
@@ -0,0 +1,2 @@
+Chromosome	Start	Stop	Reference	Variant	Transcript	Ensembl Gene ID	Variant Type	Mutation	Protein Position	Fusion Position	Gene Name	HLA Allele	Peptide Length	Sub-peptide Position	Mutation Position	MT Epitope Seq	WT Epitope Seq	Best MT Score Method	Best MT Score	Corresponding WT Score	Corresponding Fold Change	Tumor DNA Depth	Tumor DNA VAF	Tumor RNA Depth	Tumor RNA VAF	Normal Depth	Normal VAF	Gene Expression	Transcript Expression	Median MT Score	Median WT Score	Median Fold Change	NetMHC WT Score	NetMHC MT Score
+17	-1	7490589	fusion	fusion	ENST00000396501(560)-ENST00000458005	NA	frameshift_fusion	NA	NA	36	MPDU1>>GLP2R	HLA-A*29:02	9	35	NA	VLVKDVVFY	NA	NetMHC	192.74	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	192.74	NA	NA	NA	192.74
diff --git a/tests/test_data/pvacseq/fusions/MHC_Class_I/Test.final.tsv b/tests/test_data/pvacseq/fusions/MHC_Class_I/Test.final.tsv
@@ -0,0 +1,2 @@
+Chromosome	Start	Stop	Reference	Variant	Transcript	Ensembl Gene ID	Variant Type	Mutation	Protein Position	Fusion Position	Gene Name	HLA Allele	Peptide Length	Sub-peptide Position	Mutation Position	MT Epitope Seq	WT Epitope Seq	Best MT Score Method	Best MT Score	Corresponding WT Score	Corresponding Fold Change	Tumor DNA Depth	Tumor DNA VAF	Tumor RNA Depth	Tumor RNA VAF	Normal Depth	Normal VAF	Gene Expression	Transcript Expression	Median MT Score	Median WT Score	Median Fold Change	NetMHC WT Score	NetMHC MT Score
+17	-1	7490589	fusion	fusion	ENST00000396501(560)-ENST00000458005	NA	frameshift_fusion	NA	NA	36	MPDU1>>GLP2R	HLA-A*29:02	9	35	NA	VLVKDVVFY	NA	NetMHC	192.74	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	192.74	NA	NA	NA	192.74
diff --git a/tests/test_data/pvacseq/fusions/MHC_Class_I/Test.tsv b/tests/test_data/pvacseq/fusions/MHC_Class_I/Test.tsv
@@ -0,0 +1,6 @@
+chromosome_name	start	stop	reference	variant	gene_name	transcript_name	amino_acid_change	ensembl_gene_id	wildtype_amino_acid_sequence	downstream_amino_acid_sequence	fusion_amino_acid_sequence	variant_type	protein_position	fusion_position	transcript_expression	gene_expression	normal_depth	normal_vaf	tdna_depth	tdna_vaf	trna_depth	trna_vaf	index
+19	-1	39123136	fusion	fusion	EIF3K>>CYP39A1	ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016	NA	NA			QALDENMDLLEGITGFEDSVRKSSIPKNVFLALHEKLYIMLKGKMGTVNLHQFTGQLTEELHEQLENLGTHGTMDLNNLV	inframe_fusion	NA	22	NA	NA	NA	NA	NA	NA	NA	NA	EIF3K>>CYP39A1_1.inframe_fusion.22
+17	-1	7490589	fusion	fusion	MPDU1>>GLP2R	ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745	NA	NA			LLQAATNYHNGHTGQLSAITVFLLFGGSLARIFTSIQKTPLHAQLHPHELVCFFHPENPGCTGEGRRLLQLLLQEAX	frameshift_fusion	NA	37	NA	NA	NA	NA	NA	NA	NA	NA	MPDU1>>GLP2R_1.frameshift_fusion.37
+17	-1	7490589	fusion	fusion	MPDU1>>GLP2R	ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745	NA	NA			SPGSHQLPQRAHRPALSHHSLPAVWGLPGPNLHFHSENSTARATTSTX	frameshift_fusion	NA	36	NA	NA	NA	NA	NA	NA	NA	NA	MPDU1>>GLP2R_2.frameshift_fusion.36
+17	-1	7490589	fusion	fusion	MPDU1>>GLP2R	ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745	NA	NA			FSRQPPTTTTGTQASSQPSQSSCCLGAPWPESSLPFRKLHCTRNYIHMNLFASFILRTLAVLVKDVVFYNSYSKRPDNENGWMSYLSE	inframe_fusion	NA	36	NA	NA	NA	NA	NA	NA	NA	NA	MPDU1>>GLP2R_3.inframe_fusion.36
+17	-1	7490589	fusion	fusion	MPDU1>>GLP2R	ENST00000396501(560)-ENST00000458005	NA	NA			FSRQPPTTTTGTQASSQPSQSSCCLGAPWPESSLPFRKLHCTRNYIHMNLFASFILRTLAVLVKDVVFYNSYSKRPDNENGWMSYLSE	frameshift_fusion	NA	36	NA	NA	NA	NA	NA	NA	NA	NA	MPDU1>>GLP2R_3.frameshift_fusion.36
diff --git a/tests/test_data/pvacseq/fusions/MHC_Class_I/Test.tsv_1-5 b/tests/test_data/pvacseq/fusions/MHC_Class_I/Test.tsv_1-5
@@ -0,0 +1,6 @@
+chromosome_name	start	stop	reference	variant	gene_name	transcript_name	amino_acid_change	ensembl_gene_id	wildtype_amino_acid_sequence	downstream_amino_acid_sequence	fusion_amino_acid_sequence	variant_type	protein_position	fusion_position	transcript_expression	gene_expression	normal_depth	normal_vaf	tdna_depth	tdna_vaf	trna_depth	trna_vaf	index
+19	-1	39123136	fusion	fusion	EIF3K>>CYP39A1	ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016	NA	NA			QALDENMDLLEGITGFEDSVRKSSIPKNVFLALHEKLYIMLKGKMGTVNLHQFTGQLTEELHEQLENLGTHGTMDLNNLV	inframe_fusion	NA	22	NA	NA	NA	NA	NA	NA	NA	NA	EIF3K>>CYP39A1_1.inframe_fusion.22
+17	-1	7490589	fusion	fusion	MPDU1>>GLP2R	ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745	NA	NA			LLQAATNYHNGHTGQLSAITVFLLFGGSLARIFTSIQKTPLHAQLHPHELVCFFHPENPGCTGEGRRLLQLLLQEAX	frameshift_fusion	NA	37	NA	NA	NA	NA	NA	NA	NA	NA	MPDU1>>GLP2R_1.frameshift_fusion.37
+17	-1	7490589	fusion	fusion	MPDU1>>GLP2R	ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745	NA	NA			SPGSHQLPQRAHRPALSHHSLPAVWGLPGPNLHFHSENSTARATTSTX	frameshift_fusion	NA	36	NA	NA	NA	NA	NA	NA	NA	NA	MPDU1>>GLP2R_2.frameshift_fusion.36
+17	-1	7490589	fusion	fusion	MPDU1>>GLP2R	ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745	NA	NA			FSRQPPTTTTGTQASSQPSQSSCCLGAPWPESSLPFRKLHCTRNYIHMNLFASFILRTLAVLVKDVVFYNSYSKRPDNENGWMSYLSE	inframe_fusion	NA	36	NA	NA	NA	NA	NA	NA	NA	NA	MPDU1>>GLP2R_3.inframe_fusion.36
+17	-1	7490589	fusion	fusion	MPDU1>>GLP2R	ENST00000396501(560)-ENST00000458005	NA	NA			FSRQPPTTTTGTQASSQPSQSSCCLGAPWPESSLPFRKLHCTRNYIHMNLFASFILRTLAVLVKDVVFYNSYSKRPDNENGWMSYLSE	frameshift_fusion	NA	36	NA	NA	NA	NA	NA	NA	NA	NA	MPDU1>>GLP2R_3.frameshift_fusion.36