diff --git a/pvacseq/lib/pipeline.py b/pvacseq/lib/pipeline.py index 80704a2..0f9ede1 100644 --- a/pvacseq/lib/pipeline.py +++ b/pvacseq/lib/pipeline.py @@ -482,7 +482,7 @@ def call_iedb_and_parse_outputs(self, chunks): params['sample_name'] = self.sample_name else: params['sample_name'] = None - parser = DefaultOutputParser(**params) + parser = self.output_parser(params) parser.execute() status_message("Completed") split_parsed_output_files.append(split_parsed_file_path) @@ -583,7 +583,7 @@ def call_iedb_and_parse_outputs(self, chunks): params['sample_name'] = self.sample_name else: params['sample_name'] = None - parser = DefaultOutputParser(**params) + parser = self.output_parser(params) parser.execute() status_message("Completed") split_parsed_output_files.append(split_parsed_file_path) 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 new file mode 100644 index 0000000..da82899 --- /dev/null +++ b/tests/test_data/pvacseq/fusions/MHC_Class_I/Test.combined.parsed.tsv @@ -0,0 +1,133 @@ +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 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 11 NA SSIPKNVFL NA NetMHC 19395.75 NA NA NA NA NA NA NA NA NA NA 19395.75 NA NA NA 19395.75 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 12 NA SIPKNVFLA NA NetMHC 22448.14 NA NA NA NA NA NA NA NA NA NA 22448.14 NA NA NA 22448.14 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 10 NA KSSIPKNVF NA NetMHC 22972.24 NA NA NA NA NA NA NA NA NA NA 22972.24 NA NA NA 22972.24 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 3 NA GFEDSVRKS NA NetMHC 27354.62 NA NA NA NA NA NA NA NA NA NA 27354.62 NA NA NA 27354.62 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 2 NA TGFEDSVRK NA NetMHC 28705.46 NA NA NA NA NA NA NA NA NA NA 28705.46 NA NA NA 28705.46 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 7 NA SVRKSSIPK NA NetMHC 32310.45 NA NA NA NA NA NA NA NA NA NA 32310.45 NA NA NA 32310.45 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 1 NA ITGFEDSVR NA NetMHC 32640.39 NA NA NA NA NA NA NA NA NA NA 32640.39 NA NA NA 32640.39 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 4 NA FEDSVRKSS NA NetMHC 36907.69 NA NA NA NA NA NA NA NA NA NA 36907.69 NA NA NA 36907.69 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 9 NA RKSSIPKNV NA NetMHC 37337.88 NA NA NA NA NA NA NA NA NA NA 37337.88 NA NA NA 37337.88 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 5 NA EDSVRKSSI NA NetMHC 39014.61 NA NA NA NA NA NA NA NA NA NA 39014.61 NA NA NA 39014.61 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 8 NA VRKSSIPKN NA NetMHC 40002.45 NA NA NA NA NA NA NA NA NA NA 40002.45 NA NA NA 40002.45 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 6 NA DSVRKSSIP NA NetMHC 43503.33 NA NA NA NA NA NA NA NA NA NA 43503.33 NA NA NA 43503.33 +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 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 40 NA VVFYNSYSK NA NetMHC 1233.7 NA NA NA NA NA NA NA NA NA NA 1233.7 NA NA NA 1233.7 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 20 NA IHMNLFASF NA NetMHC 2748.3 NA NA NA NA NA NA NA NA NA NA 2748.3 NA NA NA 2748.3 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 17 NA RNYIHMNLF NA NetMHC 2878.03 NA NA NA NA NA NA NA NA NA NA 2878.03 NA NA NA 2878.03 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 27 NA SFILRTLAV NA NetMHC 2917.53 NA NA NA NA NA NA NA NA NA NA 2917.53 NA NA NA 2917.53 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 51 NA DNENGWMSY NA NetMHC 2999.8 NA NA NA NA NA NA NA NA NA NA 2999.8 NA NA NA 2999.8 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 18 NA NYIHMNLFA NA NetMHC 3864.1 NA NA NA NA NA NA NA NA NA NA 3864.1 NA NA NA 3864.1 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 24 NA LFASFILRT NA NetMHC 5066.74 NA NA NA NA NA NA NA NA NA NA 5066.74 NA NA NA 5066.74 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 38 NA KDVVFYNSY NA NetMHC 5130.13 NA NA NA NA NA NA NA NA NA NA 5130.13 NA NA NA 5130.13 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 23 NA NLFASFILR NA NetMHC 5346.78 NA NA NA NA NA NA NA NA NA NA 5346.78 NA NA NA 5346.78 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 21 NA HMNLFASFI NA NetMHC 5485.9 NA NA NA NA NA NA NA NA NA NA 5485.9 NA NA NA 5485.9 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 22 NA MNLFASFIL NA NetMHC 5930.73 NA NA NA NA NA NA NA NA NA NA 5930.73 NA NA NA 5930.73 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 2 NA PWPESSLPF NA NetMHC 6164.57 NA NA NA NA NA NA NA NA NA NA 6164.57 NA NA NA 6164.57 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 2 NA PWPESSLPF NA NetMHC 6164.57 NA NA NA NA NA NA NA NA NA NA 6164.57 NA NA NA 6164.57 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 19 NA YIHMNLFAS NA NetMHC 6175.25 NA NA NA NA NA NA NA NA NA NA 6175.25 NA NA NA 6175.25 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 11 NA RKLHCTRNY NA NetMHC 6419.28 NA NA NA NA NA NA NA NA NA NA 6419.28 NA NA NA 6419.28 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 11 NA RKLHCTRNY NA NetMHC 6419.28 NA NA NA NA NA NA NA NA NA NA 6419.28 NA NA NA 6419.28 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 7 NA TSIQKTPLH NA NetMHC 6937.25 NA NA NA NA NA NA NA NA NA NA 6937.25 NA NA NA 6937.25 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 41 NA VFYNSYSKR NA NetMHC 7367.47 NA NA NA NA NA NA NA NA NA NA 7367.47 NA NA NA 7367.47 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 6 NA SSLPFRKLH NA NetMHC 9612.01 NA NA NA NA NA NA NA NA NA NA 9612.01 NA NA NA 9612.01 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 6 NA SSLPFRKLH NA NetMHC 9612.01 NA NA NA NA NA NA NA NA NA NA 9612.01 NA NA NA 9612.01 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 29 NA ILRTLAVLV NA NetMHC 10219.27 NA NA NA NA NA NA NA NA NA NA 10219.27 NA NA NA 10219.27 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 1 NA LPGPNLHFH NA NetMHC 11341.87 NA NA NA NA NA NA NA NA NA NA 11341.87 NA NA NA 11341.87 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 19 NA HPHELVCFF NA NetMHC 11710.23 NA NA NA NA NA NA NA NA NA NA 11710.23 NA NA NA 11710.23 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 53 NA ENGWMSYLS NA NetMHC 12198.7 NA NA NA NA NA NA NA NA NA NA 12198.7 NA NA NA 12198.7 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 1 NA SLARIFTSI NA NetMHC 13573.08 NA NA NA NA NA NA NA NA NA NA 13573.08 NA NA NA 13573.08 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 23 NA LVCFFHPEN NA NetMHC 14006.93 NA NA NA NA NA NA NA NA NA NA 14006.93 NA NA NA 14006.93 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 13 NA PLHAQLHPH NA NetMHC 14264.95 NA NA NA NA NA NA NA NA NA NA 14264.95 NA NA NA 14264.95 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 34 NA AVLVKDVVF NA NetMHC 14303.12 NA NA NA NA NA NA NA NA NA NA 14303.12 NA NA NA 14303.12 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 6 NA FTSIQKTPL NA NetMHC 14767.49 NA NA NA NA NA NA NA NA NA NA 14767.49 NA NA NA 14767.49 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 28 NA FILRTLAVL NA NetMHC 14880.41 NA NA NA NA NA NA NA NA NA NA 14880.41 NA NA NA 14880.41 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 25 NA FASFILRTL NA NetMHC 15001.65 NA NA NA NA NA NA NA NA NA NA 15001.65 NA NA NA 15001.65 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 20 NA PHELVCFFH NA NetMHC 15450.05 NA NA NA NA NA NA NA NA NA NA 15450.05 NA NA NA 15450.05 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 26 NA ASFILRTLA NA NetMHC 15922.35 NA NA NA NA NA NA NA NA NA NA 15922.35 NA NA NA 15922.35 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 36 NA LVKDVVFYN NA NetMHC 16091.72 NA NA NA NA NA NA NA NA NA NA 16091.72 NA NA NA 16091.72 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 42 NA FYNSYSKRP NA NetMHC 17466.72 NA NA NA NA NA NA NA NA NA NA 17466.72 NA NA NA 17466.72 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 18 NA LHPHELVCF NA NetMHC 17685.21 NA NA NA NA NA NA NA NA NA NA 17685.21 NA NA NA 17685.21 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 12 NA KLHCTRNYI NA NetMHC 17834.91 NA NA NA NA NA NA NA NA NA NA 17834.91 NA NA NA 17834.91 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 12 NA KLHCTRNYI NA NetMHC 17834.91 NA NA NA NA NA NA NA NA NA NA 17834.91 NA NA NA 17834.91 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 39 NA DVVFYNSYS NA NetMHC 18470.03 NA NA NA NA NA NA NA NA NA NA 18470.03 NA NA NA 18470.03 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 40 NA RLLQLLLQE NA NetMHC 18639.47 NA NA NA NA NA NA NA NA NA NA 18639.47 NA NA NA 18639.47 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 38 NA GRRLLQLLL NA NetMHC 18719.09 NA NA NA NA NA NA NA NA NA NA 18719.09 NA NA NA 18719.09 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 25 NA CFFHPENPG NA NetMHC 18859.16 NA NA NA NA NA NA NA NA NA NA 18859.16 NA NA NA 18859.16 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 52 NA NENGWMSYL NA NetMHC 18871.2 NA NA NA NA NA NA NA NA NA NA 18871.2 NA NA NA 18871.2 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 32 NA TLAVLVKDV NA NetMHC 19139.96 NA NA NA NA NA NA NA NA NA NA 19139.96 NA NA NA 19139.96 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 11 NA KTPLHAQLH NA NetMHC 19462.19 NA NA NA NA NA NA NA NA NA NA 19462.19 NA NA NA 19462.19 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 8 NA FHSENSTAR NA NetMHC 19473.13 NA NA NA NA NA NA NA NA NA NA 19473.13 NA NA NA 19473.13 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 26 NA FFHPENPGC NA NetMHC 19611.43 NA NA NA NA NA NA NA NA NA NA 19611.43 NA NA NA 19611.43 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 22 NA ELVCFFHPE NA NetMHC 19659.65 NA NA NA NA NA NA NA NA NA NA 19659.65 NA NA NA 19659.65 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 41 NA LLQLLLQEA NA NetMHC 20143.26 NA NA NA NA NA NA NA NA NA NA 20143.26 NA NA NA 20143.26 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 16 NA TRNYIHMNL NA NetMHC 20146.52 NA NA NA NA NA NA NA NA NA NA 20146.52 NA NA NA 20146.52 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 34 NA CTGEGRRLL NA NetMHC 20179.69 NA NA NA NA NA NA NA NA NA NA 20179.69 NA NA NA 20179.69 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 13 NA LHCTRNYIH NA NetMHC 20194.32 NA NA NA NA NA NA NA NA NA NA 20194.32 NA NA NA 20194.32 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 5 NA IFTSIQKTP NA NetMHC 20883.82 NA NA NA NA NA NA NA NA NA NA 20883.82 NA NA NA 20883.82 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 15 NA HAQLHPHEL NA NetMHC 23076.37 NA NA NA NA NA NA NA NA NA NA 23076.37 NA NA NA 23076.37 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 16 NA AQLHPHELV NA NetMHC 23500.69 NA NA NA NA NA NA NA NA NA NA 23500.69 NA NA NA 23500.69 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 15 NA CTRNYIHMN NA NetMHC 23636.87 NA NA NA NA NA NA NA NA NA NA 23636.87 NA NA NA 23636.87 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 14 NA LHAQLHPHE NA NetMHC 23637.63 NA NA NA NA NA NA NA NA NA NA 23637.63 NA NA NA 23637.63 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 3 NA WPESSLPFR NA NetMHC 23668.08 NA NA NA NA NA NA NA NA NA NA 23668.08 NA NA NA 23668.08 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 3 NA WPESSLPFR NA NetMHC 23668.08 NA NA NA NA NA NA NA NA NA NA 23668.08 NA NA NA 23668.08 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 10 NA QKTPLHAQL NA NetMHC 25449.21 NA NA NA NA NA NA NA NA NA NA 25449.21 NA NA NA 25449.21 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 9 NA PFRKLHCTR NA NetMHC 25530.3 NA NA NA NA NA NA NA NA NA NA 25530.3 NA NA NA 25530.3 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 9 NA PFRKLHCTR NA NetMHC 25530.3 NA NA NA NA NA NA NA NA NA NA 25530.3 NA NA NA 25530.3 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 39 NA RRLLQLLLQ NA NetMHC 25883.82 NA NA NA NA NA NA NA NA NA NA 25883.82 NA NA NA 25883.82 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 37 NA EGRRLLQLL NA NetMHC 27215.87 NA NA NA NA NA NA NA NA NA NA 27215.87 NA NA NA 27215.87 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 8 NA SIQKTPLHA NA NetMHC 27316.47 NA NA NA NA NA NA NA NA NA NA 27316.47 NA NA NA 27316.47 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 37 NA VKDVVFYNS NA NetMHC 27386.3 NA NA NA NA NA NA NA NA NA NA 27386.3 NA NA NA 27386.3 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 7 NA HFHSENSTA NA NetMHC 27799.49 NA NA NA NA NA NA NA NA NA NA 27799.49 NA NA NA 27799.49 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 9 NA IQKTPLHAQ NA NetMHC 27827.78 NA NA NA NA NA NA NA NA NA NA 27827.78 NA NA NA 27827.78 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 21 NA HELVCFFHP NA NetMHC 27883.54 NA NA NA NA NA NA NA NA NA NA 27883.54 NA NA NA 27883.54 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 5 NA ESSLPFRKL NA NetMHC 27992.35 NA NA NA NA NA NA NA NA NA NA 27992.35 NA NA NA 27992.35 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 5 NA ESSLPFRKL NA NetMHC 27992.35 NA NA NA NA NA NA NA NA NA NA 27992.35 NA NA NA 27992.35 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 5 NA NLHFHSENS NA NetMHC 28405.47 NA NA NA NA NA NA NA NA NA NA 28405.47 NA NA NA 28405.47 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 4 NA RIFTSIQKT NA NetMHC 28568.83 NA NA NA NA NA NA NA NA NA NA 28568.83 NA NA NA 28568.83 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 13 NA STARATTST NA NetMHC 28722.86 NA NA NA NA NA NA NA NA NA NA 28722.86 NA NA NA 28722.86 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 36 NA GEGRRLLQL NA NetMHC 29248.48 NA NA NA NA NA NA NA NA NA NA 29248.48 NA NA NA 29248.48 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 43 NA YNSYSKRPD NA NetMHC 29248.78 NA NA NA NA NA NA NA NA NA NA 29248.78 NA NA NA 29248.78 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 2 NA LARIFTSIQ NA NetMHC 29477.21 NA NA NA NA NA NA NA NA NA NA 29477.21 NA NA NA 29477.21 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 54 NA NGWMSYLSE NA NetMHC 29658.61 NA NA NA NA NA NA NA NA NA NA 29658.61 NA NA NA 29658.61 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 6 NA LHFHSENST NA NetMHC 29941.06 NA NA NA NA NA NA NA NA NA NA 29941.06 NA NA NA 29941.06 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 4 NA PNLHFHSEN NA NetMHC 30313.63 NA NA NA NA NA NA NA NA NA NA 30313.63 NA NA NA 30313.63 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 46 NA YSKRPDNEN NA NetMHC 30354.99 NA NA NA NA NA NA NA NA NA NA 30354.99 NA NA NA 30354.99 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 3 NA ARIFTSIQK NA NetMHC 30561.94 NA NA NA NA NA NA NA NA NA NA 30561.94 NA NA NA 30561.94 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 35 NA TGEGRRLLQ NA NetMHC 30972.07 NA NA NA NA NA NA NA NA NA NA 30972.07 NA NA NA 30972.07 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 4 NA PESSLPFRK NA NetMHC 31208.2 NA NA NA NA NA NA NA NA NA NA 31208.2 NA NA NA 31208.2 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 4 NA PESSLPFRK NA NetMHC 31208.2 NA NA NA NA NA NA NA NA NA NA 31208.2 NA NA NA 31208.2 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 14 NA HCTRNYIHM NA NetMHC 31253.16 NA NA NA NA NA NA NA NA NA NA 31253.16 NA NA NA 31253.16 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 31 NA RTLAVLVKD NA NetMHC 31887.8 NA NA NA NA NA NA NA NA NA NA 31887.8 NA NA NA 31887.8 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 7 NA SLPFRKLHC NA NetMHC 32047.6 NA NA NA NA NA NA NA NA NA NA 32047.6 NA NA NA 32047.6 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 7 NA SLPFRKLHC NA NetMHC 32047.6 NA NA NA NA NA NA NA NA NA NA 32047.6 NA NA NA 32047.6 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 44 NA NSYSKRPDN NA NetMHC 32385.0 NA NA NA NA NA NA NA NA NA NA 32385.0 NA NA NA 32385.0 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 12 NA TPLHAQLHP NA NetMHC 32581.12 NA NA NA NA NA NA NA NA NA NA 32581.12 NA NA NA 32581.12 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 3 NA GPNLHFHSE NA NetMHC 32653.11 NA NA NA NA NA NA NA NA NA NA 32653.11 NA NA NA 32653.11 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 17 NA QLHPHELVC NA NetMHC 33029.76 NA NA NA NA NA NA NA NA NA NA 33029.76 NA NA NA 33029.76 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 30 NA LRTLAVLVK NA NetMHC 33062.67 NA NA NA NA NA NA NA NA NA NA 33062.67 NA NA NA 33062.67 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 9 NA HSENSTARA NA NetMHC 33539.71 NA NA NA NA NA NA NA NA NA NA 33539.71 NA NA NA 33539.71 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 8 NA LPFRKLHCT NA NetMHC 33598.18 NA NA NA NA NA NA NA NA NA NA 33598.18 NA NA NA 33598.18 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 8 NA LPFRKLHCT NA NetMHC 33598.18 NA NA NA NA NA NA NA NA NA NA 33598.18 NA NA NA 33598.18 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 12 NA NSTARATTS NA NetMHC 33755.58 NA NA NA NA NA NA NA NA NA NA 33755.58 NA NA NA 33755.58 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 45 NA SYSKRPDNE NA NetMHC 33779.34 NA NA NA NA NA NA NA NA NA NA 33779.34 NA NA NA 33779.34 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 27 NA FHPENPGCT NA NetMHC 34960.66 NA NA NA NA NA NA NA NA NA NA 34960.66 NA NA NA 34960.66 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 30 NA ENPGCTGEG NA NetMHC 35131.69 NA NA NA NA NA NA NA NA NA NA 35131.69 NA NA NA 35131.69 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 1 NA APWPESSLP NA NetMHC 35259.25 NA NA NA NA NA NA NA NA NA NA 35259.25 NA NA NA 35259.25 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 1 NA APWPESSLP NA NetMHC 35259.25 NA NA NA NA NA NA NA NA NA NA 35259.25 NA NA NA 35259.25 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 31 NA NPGCTGEGR NA NetMHC 35523.1 NA NA NA NA NA NA NA NA NA NA 35523.1 NA NA NA 35523.1 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 10 NA FRKLHCTRN NA NetMHC 35593.11 NA NA NA NA NA NA NA NA NA NA 35593.11 NA NA NA 35593.11 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 10 NA FRKLHCTRN NA NetMHC 35593.11 NA NA NA NA NA NA NA NA NA NA 35593.11 NA NA NA 35593.11 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 24 NA VCFFHPENP NA NetMHC 35646.29 NA NA NA NA NA NA NA NA NA NA 35646.29 NA NA NA 35646.29 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 33 NA LAVLVKDVV NA NetMHC 35679.87 NA NA NA NA NA NA NA NA NA NA 35679.87 NA NA NA 35679.87 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 2 NA PGPNLHFHS NA NetMHC 35758.72 NA NA NA NA NA NA NA NA NA NA 35758.72 NA NA NA 35758.72 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 49 NA RPDNENGWM NA NetMHC 36016.54 NA NA NA NA NA NA NA NA NA NA 36016.54 NA NA NA 36016.54 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 50 NA PDNENGWMS NA NetMHC 36173.53 NA NA NA NA NA NA NA NA NA NA 36173.53 NA NA NA 36173.53 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 11 NA ENSTARATT NA NetMHC 36936.45 NA NA NA NA NA NA NA NA NA NA 36936.45 NA NA NA 36936.45 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 10 NA SENSTARAT NA NetMHC 38042.53 NA NA NA NA NA NA NA NA NA NA 38042.53 NA NA NA 38042.53 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 33 NA GCTGEGRRL NA NetMHC 38555.95 NA NA NA NA NA NA NA NA NA NA 38555.95 NA NA NA 38555.95 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 29 NA PENPGCTGE NA NetMHC 38861.25 NA NA NA NA NA NA NA NA NA NA 38861.25 NA NA NA 38861.25 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 48 NA KRPDNENGW NA NetMHC 39757.8 NA NA NA NA NA NA NA NA NA NA 39757.8 NA NA NA 39757.8 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 32 NA PGCTGEGRR NA NetMHC 41335.19 NA NA NA NA NA NA NA NA NA NA 41335.19 NA NA NA 41335.19 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 28 NA HPENPGCTG NA NetMHC 41340.55 NA NA NA NA NA NA NA NA NA NA 41340.55 NA NA NA 41340.55 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 47 NA SKRPDNENG NA NetMHC 42436.38 NA NA NA NA NA NA NA NA NA NA 42436.38 NA NA NA 42436.38 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 new file mode 100644 index 0000000..e3854f0 --- /dev/null +++ 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 new file mode 100644 index 0000000..e3854f0 --- /dev/null +++ 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 new file mode 100644 index 0000000..df58fac --- /dev/null +++ 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 new file mode 100644 index 0000000..df58fac --- /dev/null +++ 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 diff --git a/tests/test_data/pvacseq/fusions/MHC_Class_I/tmp/Test.HLA-A*29:02.9.parsed.tsv_1-10 b/tests/test_data/pvacseq/fusions/MHC_Class_I/tmp/Test.HLA-A*29:02.9.parsed.tsv_1-10 new file mode 100644 index 0000000..3dd6886 --- /dev/null +++ b/tests/test_data/pvacseq/fusions/MHC_Class_I/tmp/Test.HLA-A*29:02.9.parsed.tsv_1-10 @@ -0,0 +1,133 @@ +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 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 11 NA SSIPKNVFL NA NetMHC 19395.75 NA NA NA NA NA NA NA NA NA NA 19395.75 NA NA NA 19395.75 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 12 NA SIPKNVFLA NA NetMHC 22448.14 NA NA NA NA NA NA NA NA NA NA 22448.14 NA NA NA 22448.14 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 10 NA KSSIPKNVF NA NetMHC 22972.24 NA NA NA NA NA NA NA NA NA NA 22972.24 NA NA NA 22972.24 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 3 NA GFEDSVRKS NA NetMHC 27354.62 NA NA NA NA NA NA NA NA NA NA 27354.62 NA NA NA 27354.62 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 2 NA TGFEDSVRK NA NetMHC 28705.46 NA NA NA NA NA NA NA NA NA NA 28705.46 NA NA NA 28705.46 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 7 NA SVRKSSIPK NA NetMHC 32310.45 NA NA NA NA NA NA NA NA NA NA 32310.45 NA NA NA 32310.45 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 1 NA ITGFEDSVR NA NetMHC 32640.39 NA NA NA NA NA NA NA NA NA NA 32640.39 NA NA NA 32640.39 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 4 NA FEDSVRKSS NA NetMHC 36907.69 NA NA NA NA NA NA NA NA NA NA 36907.69 NA NA NA 36907.69 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 9 NA RKSSIPKNV NA NetMHC 37337.88 NA NA NA NA NA NA NA NA NA NA 37337.88 NA NA NA 37337.88 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 5 NA EDSVRKSSI NA NetMHC 39014.61 NA NA NA NA NA NA NA NA NA NA 39014.61 NA NA NA 39014.61 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 8 NA VRKSSIPKN NA NetMHC 40002.45 NA NA NA NA NA NA NA NA NA NA 40002.45 NA NA NA 40002.45 +19 -1 39123136 fusion fusion ENST00000248342(421)-ENST00000275016;ENST00000538434(160)-ENST00000275016;ENST00000545173(421)-ENST00000275016;ENST00000592558(421)-ENST00000275016;ENST00000593149(160)-ENST00000275016 NA inframe_fusion NA NA 22 EIF3K>>CYP39A1 HLA-A*29:02 9 6 NA DSVRKSSIP NA NetMHC 43503.33 NA NA NA NA NA NA NA NA NA NA 43503.33 NA NA NA 43503.33 +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 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 40 NA VVFYNSYSK NA NetMHC 1233.7 NA NA NA NA NA NA NA NA NA NA 1233.7 NA NA NA 1233.7 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 20 NA IHMNLFASF NA NetMHC 2748.3 NA NA NA NA NA NA NA NA NA NA 2748.3 NA NA NA 2748.3 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 17 NA RNYIHMNLF NA NetMHC 2878.03 NA NA NA NA NA NA NA NA NA NA 2878.03 NA NA NA 2878.03 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 27 NA SFILRTLAV NA NetMHC 2917.53 NA NA NA NA NA NA NA NA NA NA 2917.53 NA NA NA 2917.53 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 51 NA DNENGWMSY NA NetMHC 2999.8 NA NA NA NA NA NA NA NA NA NA 2999.8 NA NA NA 2999.8 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 18 NA NYIHMNLFA NA NetMHC 3864.1 NA NA NA NA NA NA NA NA NA NA 3864.1 NA NA NA 3864.1 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 24 NA LFASFILRT NA NetMHC 5066.74 NA NA NA NA NA NA NA NA NA NA 5066.74 NA NA NA 5066.74 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 38 NA KDVVFYNSY NA NetMHC 5130.13 NA NA NA NA NA NA NA NA NA NA 5130.13 NA NA NA 5130.13 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 23 NA NLFASFILR NA NetMHC 5346.78 NA NA NA NA NA NA NA NA NA NA 5346.78 NA NA NA 5346.78 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 21 NA HMNLFASFI NA NetMHC 5485.9 NA NA NA NA NA NA NA NA NA NA 5485.9 NA NA NA 5485.9 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 22 NA MNLFASFIL NA NetMHC 5930.73 NA NA NA NA NA NA NA NA NA NA 5930.73 NA NA NA 5930.73 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 2 NA PWPESSLPF NA NetMHC 6164.57 NA NA NA NA NA NA NA NA NA NA 6164.57 NA NA NA 6164.57 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 2 NA PWPESSLPF NA NetMHC 6164.57 NA NA NA NA NA NA NA NA NA NA 6164.57 NA NA NA 6164.57 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 19 NA YIHMNLFAS NA NetMHC 6175.25 NA NA NA NA NA NA NA NA NA NA 6175.25 NA NA NA 6175.25 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 11 NA RKLHCTRNY NA NetMHC 6419.28 NA NA NA NA NA NA NA NA NA NA 6419.28 NA NA NA 6419.28 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 11 NA RKLHCTRNY NA NetMHC 6419.28 NA NA NA NA NA NA NA NA NA NA 6419.28 NA NA NA 6419.28 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 7 NA TSIQKTPLH NA NetMHC 6937.25 NA NA NA NA NA NA NA NA NA NA 6937.25 NA NA NA 6937.25 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 41 NA VFYNSYSKR NA NetMHC 7367.47 NA NA NA NA NA NA NA NA NA NA 7367.47 NA NA NA 7367.47 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 6 NA SSLPFRKLH NA NetMHC 9612.01 NA NA NA NA NA NA NA NA NA NA 9612.01 NA NA NA 9612.01 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 6 NA SSLPFRKLH NA NetMHC 9612.01 NA NA NA NA NA NA NA NA NA NA 9612.01 NA NA NA 9612.01 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 29 NA ILRTLAVLV NA NetMHC 10219.27 NA NA NA NA NA NA NA NA NA NA 10219.27 NA NA NA 10219.27 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 1 NA LPGPNLHFH NA NetMHC 11341.87 NA NA NA NA NA NA NA NA NA NA 11341.87 NA NA NA 11341.87 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 19 NA HPHELVCFF NA NetMHC 11710.23 NA NA NA NA NA NA NA NA NA NA 11710.23 NA NA NA 11710.23 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 53 NA ENGWMSYLS NA NetMHC 12198.7 NA NA NA NA NA NA NA NA NA NA 12198.7 NA NA NA 12198.7 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 1 NA SLARIFTSI NA NetMHC 13573.08 NA NA NA NA NA NA NA NA NA NA 13573.08 NA NA NA 13573.08 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 23 NA LVCFFHPEN NA NetMHC 14006.93 NA NA NA NA NA NA NA NA NA NA 14006.93 NA NA NA 14006.93 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 13 NA PLHAQLHPH NA NetMHC 14264.95 NA NA NA NA NA NA NA NA NA NA 14264.95 NA NA NA 14264.95 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 34 NA AVLVKDVVF NA NetMHC 14303.12 NA NA NA NA NA NA NA NA NA NA 14303.12 NA NA NA 14303.12 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 6 NA FTSIQKTPL NA NetMHC 14767.49 NA NA NA NA NA NA NA NA NA NA 14767.49 NA NA NA 14767.49 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 28 NA FILRTLAVL NA NetMHC 14880.41 NA NA NA NA NA NA NA NA NA NA 14880.41 NA NA NA 14880.41 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 25 NA FASFILRTL NA NetMHC 15001.65 NA NA NA NA NA NA NA NA NA NA 15001.65 NA NA NA 15001.65 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 20 NA PHELVCFFH NA NetMHC 15450.05 NA NA NA NA NA NA NA NA NA NA 15450.05 NA NA NA 15450.05 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 26 NA ASFILRTLA NA NetMHC 15922.35 NA NA NA NA NA NA NA NA NA NA 15922.35 NA NA NA 15922.35 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 36 NA LVKDVVFYN NA NetMHC 16091.72 NA NA NA NA NA NA NA NA NA NA 16091.72 NA NA NA 16091.72 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 42 NA FYNSYSKRP NA NetMHC 17466.72 NA NA NA NA NA NA NA NA NA NA 17466.72 NA NA NA 17466.72 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 18 NA LHPHELVCF NA NetMHC 17685.21 NA NA NA NA NA NA NA NA NA NA 17685.21 NA NA NA 17685.21 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 12 NA KLHCTRNYI NA NetMHC 17834.91 NA NA NA NA NA NA NA NA NA NA 17834.91 NA NA NA 17834.91 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 12 NA KLHCTRNYI NA NetMHC 17834.91 NA NA NA NA NA NA NA NA NA NA 17834.91 NA NA NA 17834.91 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 39 NA DVVFYNSYS NA NetMHC 18470.03 NA NA NA NA NA NA NA NA NA NA 18470.03 NA NA NA 18470.03 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 40 NA RLLQLLLQE NA NetMHC 18639.47 NA NA NA NA NA NA NA NA NA NA 18639.47 NA NA NA 18639.47 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 38 NA GRRLLQLLL NA NetMHC 18719.09 NA NA NA NA NA NA NA NA NA NA 18719.09 NA NA NA 18719.09 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 25 NA CFFHPENPG NA NetMHC 18859.16 NA NA NA NA NA NA NA NA NA NA 18859.16 NA NA NA 18859.16 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 52 NA NENGWMSYL NA NetMHC 18871.2 NA NA NA NA NA NA NA NA NA NA 18871.2 NA NA NA 18871.2 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 32 NA TLAVLVKDV NA NetMHC 19139.96 NA NA NA NA NA NA NA NA NA NA 19139.96 NA NA NA 19139.96 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 11 NA KTPLHAQLH NA NetMHC 19462.19 NA NA NA NA NA NA NA NA NA NA 19462.19 NA NA NA 19462.19 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 8 NA FHSENSTAR NA NetMHC 19473.13 NA NA NA NA NA NA NA NA NA NA 19473.13 NA NA NA 19473.13 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 26 NA FFHPENPGC NA NetMHC 19611.43 NA NA NA NA NA NA NA NA NA NA 19611.43 NA NA NA 19611.43 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 22 NA ELVCFFHPE NA NetMHC 19659.65 NA NA NA NA NA NA NA NA NA NA 19659.65 NA NA NA 19659.65 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 41 NA LLQLLLQEA NA NetMHC 20143.26 NA NA NA NA NA NA NA NA NA NA 20143.26 NA NA NA 20143.26 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 16 NA TRNYIHMNL NA NetMHC 20146.52 NA NA NA NA NA NA NA NA NA NA 20146.52 NA NA NA 20146.52 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 34 NA CTGEGRRLL NA NetMHC 20179.69 NA NA NA NA NA NA NA NA NA NA 20179.69 NA NA NA 20179.69 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 13 NA LHCTRNYIH NA NetMHC 20194.32 NA NA NA NA NA NA NA NA NA NA 20194.32 NA NA NA 20194.32 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 5 NA IFTSIQKTP NA NetMHC 20883.82 NA NA NA NA NA NA NA NA NA NA 20883.82 NA NA NA 20883.82 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 15 NA HAQLHPHEL NA NetMHC 23076.37 NA NA NA NA NA NA NA NA NA NA 23076.37 NA NA NA 23076.37 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 16 NA AQLHPHELV NA NetMHC 23500.69 NA NA NA NA NA NA NA NA NA NA 23500.69 NA NA NA 23500.69 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 15 NA CTRNYIHMN NA NetMHC 23636.87 NA NA NA NA NA NA NA NA NA NA 23636.87 NA NA NA 23636.87 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 14 NA LHAQLHPHE NA NetMHC 23637.63 NA NA NA NA NA NA NA NA NA NA 23637.63 NA NA NA 23637.63 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 3 NA WPESSLPFR NA NetMHC 23668.08 NA NA NA NA NA NA NA NA NA NA 23668.08 NA NA NA 23668.08 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 3 NA WPESSLPFR NA NetMHC 23668.08 NA NA NA NA NA NA NA NA NA NA 23668.08 NA NA NA 23668.08 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 10 NA QKTPLHAQL NA NetMHC 25449.21 NA NA NA NA NA NA NA NA NA NA 25449.21 NA NA NA 25449.21 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 9 NA PFRKLHCTR NA NetMHC 25530.3 NA NA NA NA NA NA NA NA NA NA 25530.3 NA NA NA 25530.3 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 9 NA PFRKLHCTR NA NetMHC 25530.3 NA NA NA NA NA NA NA NA NA NA 25530.3 NA NA NA 25530.3 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 39 NA RRLLQLLLQ NA NetMHC 25883.82 NA NA NA NA NA NA NA NA NA NA 25883.82 NA NA NA 25883.82 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 37 NA EGRRLLQLL NA NetMHC 27215.87 NA NA NA NA NA NA NA NA NA NA 27215.87 NA NA NA 27215.87 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 8 NA SIQKTPLHA NA NetMHC 27316.47 NA NA NA NA NA NA NA NA NA NA 27316.47 NA NA NA 27316.47 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 37 NA VKDVVFYNS NA NetMHC 27386.3 NA NA NA NA NA NA NA NA NA NA 27386.3 NA NA NA 27386.3 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 7 NA HFHSENSTA NA NetMHC 27799.49 NA NA NA NA NA NA NA NA NA NA 27799.49 NA NA NA 27799.49 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 9 NA IQKTPLHAQ NA NetMHC 27827.78 NA NA NA NA NA NA NA NA NA NA 27827.78 NA NA NA 27827.78 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 21 NA HELVCFFHP NA NetMHC 27883.54 NA NA NA NA NA NA NA NA NA NA 27883.54 NA NA NA 27883.54 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 5 NA ESSLPFRKL NA NetMHC 27992.35 NA NA NA NA NA NA NA NA NA NA 27992.35 NA NA NA 27992.35 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 5 NA ESSLPFRKL NA NetMHC 27992.35 NA NA NA NA NA NA NA NA NA NA 27992.35 NA NA NA 27992.35 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 5 NA NLHFHSENS NA NetMHC 28405.47 NA NA NA NA NA NA NA NA NA NA 28405.47 NA NA NA 28405.47 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 4 NA RIFTSIQKT NA NetMHC 28568.83 NA NA NA NA NA NA NA NA NA NA 28568.83 NA NA NA 28568.83 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 13 NA STARATTST NA NetMHC 28722.86 NA NA NA NA NA NA NA NA NA NA 28722.86 NA NA NA 28722.86 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 36 NA GEGRRLLQL NA NetMHC 29248.48 NA NA NA NA NA NA NA NA NA NA 29248.48 NA NA NA 29248.48 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 43 NA YNSYSKRPD NA NetMHC 29248.78 NA NA NA NA NA NA NA NA NA NA 29248.78 NA NA NA 29248.78 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 2 NA LARIFTSIQ NA NetMHC 29477.21 NA NA NA NA NA NA NA NA NA NA 29477.21 NA NA NA 29477.21 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 54 NA NGWMSYLSE NA NetMHC 29658.61 NA NA NA NA NA NA NA NA NA NA 29658.61 NA NA NA 29658.61 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 6 NA LHFHSENST NA NetMHC 29941.06 NA NA NA NA NA NA NA NA NA NA 29941.06 NA NA NA 29941.06 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 4 NA PNLHFHSEN NA NetMHC 30313.63 NA NA NA NA NA NA NA NA NA NA 30313.63 NA NA NA 30313.63 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 46 NA YSKRPDNEN NA NetMHC 30354.99 NA NA NA NA NA NA NA NA NA NA 30354.99 NA NA NA 30354.99 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 3 NA ARIFTSIQK NA NetMHC 30561.94 NA NA NA NA NA NA NA NA NA NA 30561.94 NA NA NA 30561.94 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 35 NA TGEGRRLLQ NA NetMHC 30972.07 NA NA NA NA NA NA NA NA NA NA 30972.07 NA NA NA 30972.07 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 4 NA PESSLPFRK NA NetMHC 31208.2 NA NA NA NA NA NA NA NA NA NA 31208.2 NA NA NA 31208.2 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 4 NA PESSLPFRK NA NetMHC 31208.2 NA NA NA NA NA NA NA NA NA NA 31208.2 NA NA NA 31208.2 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 14 NA HCTRNYIHM NA NetMHC 31253.16 NA NA NA NA NA NA NA NA NA NA 31253.16 NA NA NA 31253.16 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 31 NA RTLAVLVKD NA NetMHC 31887.8 NA NA NA NA NA NA NA NA NA NA 31887.8 NA NA NA 31887.8 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 7 NA SLPFRKLHC NA NetMHC 32047.6 NA NA NA NA NA NA NA NA NA NA 32047.6 NA NA NA 32047.6 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 7 NA SLPFRKLHC NA NetMHC 32047.6 NA NA NA NA NA NA NA NA NA NA 32047.6 NA NA NA 32047.6 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 44 NA NSYSKRPDN NA NetMHC 32385.0 NA NA NA NA NA NA NA NA NA NA 32385.0 NA NA NA 32385.0 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 12 NA TPLHAQLHP NA NetMHC 32581.12 NA NA NA NA NA NA NA NA NA NA 32581.12 NA NA NA 32581.12 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 3 NA GPNLHFHSE NA NetMHC 32653.11 NA NA NA NA NA NA NA NA NA NA 32653.11 NA NA NA 32653.11 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 17 NA QLHPHELVC NA NetMHC 33029.76 NA NA NA NA NA NA NA NA NA NA 33029.76 NA NA NA 33029.76 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 30 NA LRTLAVLVK NA NetMHC 33062.67 NA NA NA NA NA NA NA NA NA NA 33062.67 NA NA NA 33062.67 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 9 NA HSENSTARA NA NetMHC 33539.71 NA NA NA NA NA NA NA NA NA NA 33539.71 NA NA NA 33539.71 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 8 NA LPFRKLHCT NA NetMHC 33598.18 NA NA NA NA NA NA NA NA NA NA 33598.18 NA NA NA 33598.18 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 8 NA LPFRKLHCT NA NetMHC 33598.18 NA NA NA NA NA NA NA NA NA NA 33598.18 NA NA NA 33598.18 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 12 NA NSTARATTS NA NetMHC 33755.58 NA NA NA NA NA NA NA NA NA NA 33755.58 NA NA NA 33755.58 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 45 NA SYSKRPDNE NA NetMHC 33779.34 NA NA NA NA NA NA NA NA NA NA 33779.34 NA NA NA 33779.34 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 27 NA FHPENPGCT NA NetMHC 34960.66 NA NA NA NA NA NA NA NA NA NA 34960.66 NA NA NA 34960.66 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 30 NA ENPGCTGEG NA NetMHC 35131.69 NA NA NA NA NA NA NA NA NA NA 35131.69 NA NA NA 35131.69 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 1 NA APWPESSLP NA NetMHC 35259.25 NA NA NA NA NA NA NA NA NA NA 35259.25 NA NA NA 35259.25 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 1 NA APWPESSLP NA NetMHC 35259.25 NA NA NA NA NA NA NA NA NA NA 35259.25 NA NA NA 35259.25 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 31 NA NPGCTGEGR NA NetMHC 35523.1 NA NA NA NA NA NA NA NA NA NA 35523.1 NA NA NA 35523.1 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 10 NA FRKLHCTRN NA NetMHC 35593.11 NA NA NA NA NA NA NA NA NA NA 35593.11 NA NA NA 35593.11 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000262441;ENST00000396501(560)-ENST00000574745 NA inframe_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 10 NA FRKLHCTRN NA NetMHC 35593.11 NA NA NA NA NA NA NA NA NA NA 35593.11 NA NA NA 35593.11 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 24 NA VCFFHPENP NA NetMHC 35646.29 NA NA NA NA NA NA NA NA NA NA 35646.29 NA NA NA 35646.29 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 33 NA LAVLVKDVV NA NetMHC 35679.87 NA NA NA NA NA NA NA NA NA NA 35679.87 NA NA NA 35679.87 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 2 NA PGPNLHFHS NA NetMHC 35758.72 NA NA NA NA NA NA NA NA NA NA 35758.72 NA NA NA 35758.72 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 49 NA RPDNENGWM NA NetMHC 36016.54 NA NA NA NA NA NA NA NA NA NA 36016.54 NA NA NA 36016.54 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 50 NA PDNENGWMS NA NetMHC 36173.53 NA NA NA NA NA NA NA NA NA NA 36173.53 NA NA NA 36173.53 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 11 NA ENSTARATT NA NetMHC 36936.45 NA NA NA NA NA NA NA NA NA NA 36936.45 NA NA NA 36936.45 +17 -1 7490589 fusion fusion ENST00000423172(532)-ENST00000262441;ENST00000423172(532)-ENST00000458005;ENST00000423172(532)-ENST00000574745 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 10 NA SENSTARAT NA NetMHC 38042.53 NA NA NA NA NA NA NA NA NA NA 38042.53 NA NA NA 38042.53 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 33 NA GCTGEGRRL NA NetMHC 38555.95 NA NA NA NA NA NA NA NA NA NA 38555.95 NA NA NA 38555.95 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 29 NA PENPGCTGE NA NetMHC 38861.25 NA NA NA NA NA NA NA NA NA NA 38861.25 NA NA NA 38861.25 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 48 NA KRPDNENGW NA NetMHC 39757.8 NA NA NA NA NA NA NA NA NA NA 39757.8 NA NA NA 39757.8 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 32 NA PGCTGEGRR NA NetMHC 41335.19 NA NA NA NA NA NA NA NA NA NA 41335.19 NA NA NA 41335.19 +17 -1 7490589 fusion fusion ENST00000250124(618)-ENST00000262441;ENST00000250124(618)-ENST00000458005;ENST00000250124(618)-ENST00000574745 NA frameshift_fusion NA NA 37 MPDU1>>GLP2R HLA-A*29:02 9 28 NA HPENPGCTG NA NetMHC 41340.55 NA NA NA NA NA NA NA NA NA NA 41340.55 NA NA NA 41340.55 +17 -1 7490589 fusion fusion ENST00000396501(560)-ENST00000458005 NA frameshift_fusion NA NA 36 MPDU1>>GLP2R HLA-A*29:02 9 47 NA SKRPDNENG NA NetMHC 42436.38 NA NA NA NA NA NA NA NA NA NA 42436.38 NA NA NA 42436.38 diff --git a/tests/test_data/pvacseq/fusions/MHC_Class_I/tmp/Test.ann.HLA-A*29:02.9.tsv_1-10 b/tests/test_data/pvacseq/fusions/MHC_Class_I/tmp/Test.ann.HLA-A*29:02.9.tsv_1-10 new file mode 100644 index 0000000..5274161 --- /dev/null +++ b/tests/test_data/pvacseq/fusions/MHC_Class_I/tmp/Test.ann.HLA-A*29:02.9.tsv_1-10 @@ -0,0 +1,133 @@ +allele seq_num start end length peptide ic50 percentile rank +HLA-A*29:02 5 35 43 9 VLVKDVVFY 192.74 0.4 +HLA-A*29:02 5 40 48 9 VVFYNSYSK 1233.70 1.2 +HLA-A*29:02 5 20 28 9 IHMNLFASF 2748.30 1.7 +HLA-A*29:02 5 17 25 9 RNYIHMNLF 2878.03 1.7 +HLA-A*29:02 5 27 35 9 SFILRTLAV 2917.53 1.7 +HLA-A*29:02 5 51 59 9 DNENGWMSY 2999.80 1.7 +HLA-A*29:02 5 18 26 9 NYIHMNLFA 3864.10 1.9 +HLA-A*29:02 5 24 32 9 LFASFILRT 5066.74 2 +HLA-A*29:02 5 38 46 9 KDVVFYNSY 5130.13 2 +HLA-A*29:02 5 23 31 9 NLFASFILR 5346.78 2 +HLA-A*29:02 5 21 29 9 HMNLFASFI 5485.90 2 +HLA-A*29:02 5 22 30 9 MNLFASFIL 5930.73 2 +HLA-A*29:02 4 2 10 9 PWPESSLPF 6164.57 2.1 +HLA-A*29:02 5 2 10 9 PWPESSLPF 6164.57 2.1 +HLA-A*29:02 5 19 27 9 YIHMNLFAS 6175.25 2.1 +HLA-A*29:02 4 11 19 9 RKLHCTRNY 6419.28 2.1 +HLA-A*29:02 5 11 19 9 RKLHCTRNY 6419.28 2.1 +HLA-A*29:02 2 7 15 9 TSIQKTPLH 6937.25 2.1 +HLA-A*29:02 5 41 49 9 VFYNSYSKR 7367.47 2.1 +HLA-A*29:02 4 6 14 9 SSLPFRKLH 9612.01 2.4 +HLA-A*29:02 5 6 14 9 SSLPFRKLH 9612.01 2.4 +HLA-A*29:02 5 29 37 9 ILRTLAVLV 10219.27 2.6 +HLA-A*29:02 3 1 9 9 LPGPNLHFH 11341.87 3.8 +HLA-A*29:02 2 19 27 9 HPHELVCFF 11710.23 4.2 +HLA-A*29:02 5 53 61 9 ENGWMSYLS 12198.70 4.7 +HLA-A*29:02 2 1 9 9 SLARIFTSI 13573.08 6.5 +HLA-A*29:02 2 23 31 9 LVCFFHPEN 14006.93 7.1 +HLA-A*29:02 2 13 21 9 PLHAQLHPH 14264.95 7.4 +HLA-A*29:02 5 34 42 9 AVLVKDVVF 14303.12 7.4 +HLA-A*29:02 2 6 14 9 FTSIQKTPL 14767.49 8.2 +HLA-A*29:02 5 28 36 9 FILRTLAVL 14880.41 8.4 +HLA-A*29:02 5 25 33 9 FASFILRTL 15001.65 8.6 +HLA-A*29:02 2 20 28 9 PHELVCFFH 15450.05 9.2 +HLA-A*29:02 5 26 34 9 ASFILRTLA 15922.35 9.5 +HLA-A*29:02 5 36 44 9 LVKDVVFYN 16091.72 9.7 +HLA-A*29:02 5 42 50 9 FYNSYSKRP 17466.72 24 +HLA-A*29:02 2 18 26 9 LHPHELVCF 17685.21 24 +HLA-A*29:02 4 12 20 9 KLHCTRNYI 17834.91 24 +HLA-A*29:02 5 12 20 9 KLHCTRNYI 17834.91 24 +HLA-A*29:02 5 39 47 9 DVVFYNSYS 18470.03 26 +HLA-A*29:02 2 40 48 9 RLLQLLLQE 18639.47 26 +HLA-A*29:02 2 38 46 9 GRRLLQLLL 18719.09 26 +HLA-A*29:02 2 25 33 9 CFFHPENPG 18859.16 26 +HLA-A*29:02 5 52 60 9 NENGWMSYL 18871.20 26 +HLA-A*29:02 5 32 40 9 TLAVLVKDV 19139.96 27 +HLA-A*29:02 1 11 19 9 SSIPKNVFL 19395.75 28 +HLA-A*29:02 2 11 19 9 KTPLHAQLH 19462.19 28 +HLA-A*29:02 3 8 16 9 FHSENSTAR 19473.13 28 +HLA-A*29:02 2 26 34 9 FFHPENPGC 19611.43 28 +HLA-A*29:02 2 22 30 9 ELVCFFHPE 19659.65 28 +HLA-A*29:02 2 41 49 9 LLQLLLQEA 20143.26 29 +HLA-A*29:02 5 16 24 9 TRNYIHMNL 20146.52 29 +HLA-A*29:02 2 34 42 9 CTGEGRRLL 20179.69 29 +HLA-A*29:02 5 13 21 9 LHCTRNYIH 20194.32 30 +HLA-A*29:02 2 5 13 9 IFTSIQKTP 20883.82 31 +HLA-A*29:02 1 12 20 9 SIPKNVFLA 22448.14 34 +HLA-A*29:02 1 10 18 9 KSSIPKNVF 22972.24 35 +HLA-A*29:02 2 15 23 9 HAQLHPHEL 23076.37 35 +HLA-A*29:02 2 16 24 9 AQLHPHELV 23500.69 36 +HLA-A*29:02 5 15 23 9 CTRNYIHMN 23636.87 37 +HLA-A*29:02 2 14 22 9 LHAQLHPHE 23637.63 37 +HLA-A*29:02 4 3 11 9 WPESSLPFR 23668.08 37 +HLA-A*29:02 5 3 11 9 WPESSLPFR 23668.08 37 +HLA-A*29:02 2 10 18 9 QKTPLHAQL 25449.21 42 +HLA-A*29:02 4 9 17 9 PFRKLHCTR 25530.30 42 +HLA-A*29:02 5 9 17 9 PFRKLHCTR 25530.30 42 +HLA-A*29:02 2 39 47 9 RRLLQLLLQ 25883.82 43 +HLA-A*29:02 2 37 45 9 EGRRLLQLL 27215.87 47 +HLA-A*29:02 2 8 16 9 SIQKTPLHA 27316.47 47 +HLA-A*29:02 1 3 11 9 GFEDSVRKS 27354.62 47 +HLA-A*29:02 5 37 45 9 VKDVVFYNS 27386.30 47 +HLA-A*29:02 3 7 15 9 HFHSENSTA 27799.49 49 +HLA-A*29:02 2 9 17 9 IQKTPLHAQ 27827.78 49 +HLA-A*29:02 2 21 29 9 HELVCFFHP 27883.54 49 +HLA-A*29:02 4 5 13 9 ESSLPFRKL 27992.35 50 +HLA-A*29:02 5 5 13 9 ESSLPFRKL 27992.35 50 +HLA-A*29:02 3 5 13 9 NLHFHSENS 28405.47 51 +HLA-A*29:02 2 4 12 9 RIFTSIQKT 28568.83 52 +HLA-A*29:02 1 2 10 9 TGFEDSVRK 28705.46 52 +HLA-A*29:02 3 13 21 9 STARATTST 28722.86 52 +HLA-A*29:02 2 36 44 9 GEGRRLLQL 29248.48 54 +HLA-A*29:02 5 43 51 9 YNSYSKRPD 29248.78 54 +HLA-A*29:02 2 2 10 9 LARIFTSIQ 29477.21 55 +HLA-A*29:02 5 54 62 9 NGWMSYLSE 29658.61 55 +HLA-A*29:02 3 6 14 9 LHFHSENST 29941.06 56 +HLA-A*29:02 3 4 12 9 PNLHFHSEN 30313.63 58 +HLA-A*29:02 5 46 54 9 YSKRPDNEN 30354.99 58 +HLA-A*29:02 2 3 11 9 ARIFTSIQK 30561.94 59 +HLA-A*29:02 2 35 43 9 TGEGRRLLQ 30972.07 61 +HLA-A*29:02 4 4 12 9 PESSLPFRK 31208.20 61 +HLA-A*29:02 5 4 12 9 PESSLPFRK 31208.20 61 +HLA-A*29:02 5 14 22 9 HCTRNYIHM 31253.16 62 +HLA-A*29:02 5 31 39 9 RTLAVLVKD 31887.80 64 +HLA-A*29:02 4 7 15 9 SLPFRKLHC 32047.60 65 +HLA-A*29:02 5 7 15 9 SLPFRKLHC 32047.60 65 +HLA-A*29:02 1 7 15 9 SVRKSSIPK 32310.45 66 +HLA-A*29:02 5 44 52 9 NSYSKRPDN 32385.00 66 +HLA-A*29:02 2 12 20 9 TPLHAQLHP 32581.12 67 +HLA-A*29:02 1 1 9 9 ITGFEDSVR 32640.39 67 +HLA-A*29:02 3 3 11 9 GPNLHFHSE 32653.11 67 +HLA-A*29:02 2 17 25 9 QLHPHELVC 33029.76 69 +HLA-A*29:02 5 30 38 9 LRTLAVLVK 33062.67 69 +HLA-A*29:02 3 9 17 9 HSENSTARA 33539.71 71 +HLA-A*29:02 4 8 16 9 LPFRKLHCT 33598.18 71 +HLA-A*29:02 5 8 16 9 LPFRKLHCT 33598.18 71 +HLA-A*29:02 3 12 20 9 NSTARATTS 33755.58 72 +HLA-A*29:02 5 45 53 9 SYSKRPDNE 33779.34 72 +HLA-A*29:02 2 27 35 9 FHPENPGCT 34960.66 76 +HLA-A*29:02 2 30 38 9 ENPGCTGEG 35131.69 76 +HLA-A*29:02 4 1 9 9 APWPESSLP 35259.25 77 +HLA-A*29:02 5 1 9 9 APWPESSLP 35259.25 77 +HLA-A*29:02 2 31 39 9 NPGCTGEGR 35523.10 78 +HLA-A*29:02 4 10 18 9 FRKLHCTRN 35593.11 78 +HLA-A*29:02 5 10 18 9 FRKLHCTRN 35593.11 78 +HLA-A*29:02 2 24 32 9 VCFFHPENP 35646.29 78 +HLA-A*29:02 5 33 41 9 LAVLVKDVV 35679.87 78 +HLA-A*29:02 3 2 10 9 PGPNLHFHS 35758.72 78 +HLA-A*29:02 5 49 57 9 RPDNENGWM 36016.54 79 +HLA-A*29:02 5 50 58 9 PDNENGWMS 36173.53 79 +HLA-A*29:02 1 4 12 9 FEDSVRKSS 36907.69 83 +HLA-A*29:02 3 11 19 9 ENSTARATT 36936.45 83 +HLA-A*29:02 1 9 17 9 RKSSIPKNV 37337.88 85 +HLA-A*29:02 3 10 18 9 SENSTARAT 38042.53 88 +HLA-A*29:02 2 33 41 9 GCTGEGRRL 38555.95 90 +HLA-A*29:02 2 29 37 9 PENPGCTGE 38861.25 91 +HLA-A*29:02 1 5 13 9 EDSVRKSSI 39014.61 92 +HLA-A*29:02 5 48 56 9 KRPDNENGW 39757.80 94 +HLA-A*29:02 1 8 16 9 VRKSSIPKN 40002.45 95 +HLA-A*29:02 2 32 40 9 PGCTGEGRR 41335.19 99 +HLA-A*29:02 2 28 36 9 HPENPGCTG 41340.55 99 +HLA-A*29:02 5 47 55 9 SKRPDNENG 42436.38 100 +HLA-A*29:02 1 6 14 9 DSVRKSSIP 43503.33 100 diff --git a/tests/test_data/pvacseq/fusions/MHC_Class_I/tmp/Test_21.fa.split_1-10 b/tests/test_data/pvacseq/fusions/MHC_Class_I/tmp/Test_21.fa.split_1-10 new file mode 100644 index 0000000..f59f871 --- /dev/null +++ b/tests/test_data/pvacseq/fusions/MHC_Class_I/tmp/Test_21.fa.split_1-10 @@ -0,0 +1,10 @@ +>1 +ITGFEDSVRKSSIPKNVFLA +>2 +SLARIFTSIQKTPLHAQLHPHELVCFFHPENPGCTGEGRRLLQLLLQEA +>3 +LPGPNLHFHSENSTARATTST +>4 +APWPESSLPFRKLHCTRNYI +>5 +APWPESSLPFRKLHCTRNYIHMNLFASFILRTLAVLVKDVVFYNSYSKRPDNENGWMSYLSE diff --git a/tests/test_data/pvacseq/fusions/MHC_Class_I/tmp/Test_21.fa.split_1-10.key b/tests/test_data/pvacseq/fusions/MHC_Class_I/tmp/Test_21.fa.split_1-10.key new file mode 100644 index 0000000..448d6f1 --- /dev/null +++ b/tests/test_data/pvacseq/fusions/MHC_Class_I/tmp/Test_21.fa.split_1-10.key @@ -0,0 +1,10 @@ +1: +- EIF3K>>CYP39A1_1.inframe_fusion.22 +2: +- MPDU1>>GLP2R_1.frameshift_fusion.37 +3: +- MPDU1>>GLP2R_2.frameshift_fusion.36 +4: +- MPDU1>>GLP2R_3.inframe_fusion.36 +5: +- MPDU1>>GLP2R_3.frameshift_fusion.36 diff --git a/tests/test_data/pvacseq/fusions_annotated.bedpe b/tests/test_data/pvacseq/fusions_annotated.bedpe new file mode 100644 index 0000000..123e359 --- /dev/null +++ b/tests/test_data/pvacseq/fusions_annotated.bedpe @@ -0,0 +1,2 @@ +19 -1 39123136 6 -1 46607405 EIF3K>>CYP39A1 1 + - 2 1 1 QALDENMDLLEGITGFEDSVRKSSIPKNVFLALHEKLYIMLKGKMGTVNLHQFTGQLTEELHEQLENLGTHGTMDLNNLV 22 1 ENST00000248342(421)|ENST00000538434(160)|ENST00000545173(421)|ENST00000592558(421)|ENST00000593149(160);ENST00000275016; 1 +17 -1 7490589 17 9760739 -1 MPDU1>>GLP2R 3 + + 4 1 1 LLQAATNYHNGHTGQLSAITVFLLFGGSLARIFTSIQKTPLHAQLHPHELVCFFHPENPGCTGEGRRLLQLLLQEAX,SPGSHQLPQRAHRPALSHHSLPAVWGLPGPNLHFHSENSTARATTSTX,FSRQPPTTTTGTQASSQPSQSSCCLGAPWPESSLPFRKLHCTRNYIHMNLFASFILRTLAVLVKDVVFYNSYSKRPDNENGWMSYLSE 37,36,36 0,1,2 ENST00000250124(618);;ENST00000262441|ENST00000458005|ENST00000574745,ENST00000423172(532);;ENST00000262441|ENST00000458005|ENST00000574745,ENST00000396501(560);ENST00000262441|ENST00000574745;ENST00000458005 1 diff --git a/tests/test_data/pvacseq/response_HLA-A*29:02_9_ann.tsv b/tests/test_data/pvacseq/response_HLA-A*29:02_9_ann.tsv new file mode 100644 index 0000000..5274161 --- /dev/null +++ b/tests/test_data/pvacseq/response_HLA-A*29:02_9_ann.tsv @@ -0,0 +1,133 @@ +allele seq_num start end length peptide ic50 percentile rank +HLA-A*29:02 5 35 43 9 VLVKDVVFY 192.74 0.4 +HLA-A*29:02 5 40 48 9 VVFYNSYSK 1233.70 1.2 +HLA-A*29:02 5 20 28 9 IHMNLFASF 2748.30 1.7 +HLA-A*29:02 5 17 25 9 RNYIHMNLF 2878.03 1.7 +HLA-A*29:02 5 27 35 9 SFILRTLAV 2917.53 1.7 +HLA-A*29:02 5 51 59 9 DNENGWMSY 2999.80 1.7 +HLA-A*29:02 5 18 26 9 NYIHMNLFA 3864.10 1.9 +HLA-A*29:02 5 24 32 9 LFASFILRT 5066.74 2 +HLA-A*29:02 5 38 46 9 KDVVFYNSY 5130.13 2 +HLA-A*29:02 5 23 31 9 NLFASFILR 5346.78 2 +HLA-A*29:02 5 21 29 9 HMNLFASFI 5485.90 2 +HLA-A*29:02 5 22 30 9 MNLFASFIL 5930.73 2 +HLA-A*29:02 4 2 10 9 PWPESSLPF 6164.57 2.1 +HLA-A*29:02 5 2 10 9 PWPESSLPF 6164.57 2.1 +HLA-A*29:02 5 19 27 9 YIHMNLFAS 6175.25 2.1 +HLA-A*29:02 4 11 19 9 RKLHCTRNY 6419.28 2.1 +HLA-A*29:02 5 11 19 9 RKLHCTRNY 6419.28 2.1 +HLA-A*29:02 2 7 15 9 TSIQKTPLH 6937.25 2.1 +HLA-A*29:02 5 41 49 9 VFYNSYSKR 7367.47 2.1 +HLA-A*29:02 4 6 14 9 SSLPFRKLH 9612.01 2.4 +HLA-A*29:02 5 6 14 9 SSLPFRKLH 9612.01 2.4 +HLA-A*29:02 5 29 37 9 ILRTLAVLV 10219.27 2.6 +HLA-A*29:02 3 1 9 9 LPGPNLHFH 11341.87 3.8 +HLA-A*29:02 2 19 27 9 HPHELVCFF 11710.23 4.2 +HLA-A*29:02 5 53 61 9 ENGWMSYLS 12198.70 4.7 +HLA-A*29:02 2 1 9 9 SLARIFTSI 13573.08 6.5 +HLA-A*29:02 2 23 31 9 LVCFFHPEN 14006.93 7.1 +HLA-A*29:02 2 13 21 9 PLHAQLHPH 14264.95 7.4 +HLA-A*29:02 5 34 42 9 AVLVKDVVF 14303.12 7.4 +HLA-A*29:02 2 6 14 9 FTSIQKTPL 14767.49 8.2 +HLA-A*29:02 5 28 36 9 FILRTLAVL 14880.41 8.4 +HLA-A*29:02 5 25 33 9 FASFILRTL 15001.65 8.6 +HLA-A*29:02 2 20 28 9 PHELVCFFH 15450.05 9.2 +HLA-A*29:02 5 26 34 9 ASFILRTLA 15922.35 9.5 +HLA-A*29:02 5 36 44 9 LVKDVVFYN 16091.72 9.7 +HLA-A*29:02 5 42 50 9 FYNSYSKRP 17466.72 24 +HLA-A*29:02 2 18 26 9 LHPHELVCF 17685.21 24 +HLA-A*29:02 4 12 20 9 KLHCTRNYI 17834.91 24 +HLA-A*29:02 5 12 20 9 KLHCTRNYI 17834.91 24 +HLA-A*29:02 5 39 47 9 DVVFYNSYS 18470.03 26 +HLA-A*29:02 2 40 48 9 RLLQLLLQE 18639.47 26 +HLA-A*29:02 2 38 46 9 GRRLLQLLL 18719.09 26 +HLA-A*29:02 2 25 33 9 CFFHPENPG 18859.16 26 +HLA-A*29:02 5 52 60 9 NENGWMSYL 18871.20 26 +HLA-A*29:02 5 32 40 9 TLAVLVKDV 19139.96 27 +HLA-A*29:02 1 11 19 9 SSIPKNVFL 19395.75 28 +HLA-A*29:02 2 11 19 9 KTPLHAQLH 19462.19 28 +HLA-A*29:02 3 8 16 9 FHSENSTAR 19473.13 28 +HLA-A*29:02 2 26 34 9 FFHPENPGC 19611.43 28 +HLA-A*29:02 2 22 30 9 ELVCFFHPE 19659.65 28 +HLA-A*29:02 2 41 49 9 LLQLLLQEA 20143.26 29 +HLA-A*29:02 5 16 24 9 TRNYIHMNL 20146.52 29 +HLA-A*29:02 2 34 42 9 CTGEGRRLL 20179.69 29 +HLA-A*29:02 5 13 21 9 LHCTRNYIH 20194.32 30 +HLA-A*29:02 2 5 13 9 IFTSIQKTP 20883.82 31 +HLA-A*29:02 1 12 20 9 SIPKNVFLA 22448.14 34 +HLA-A*29:02 1 10 18 9 KSSIPKNVF 22972.24 35 +HLA-A*29:02 2 15 23 9 HAQLHPHEL 23076.37 35 +HLA-A*29:02 2 16 24 9 AQLHPHELV 23500.69 36 +HLA-A*29:02 5 15 23 9 CTRNYIHMN 23636.87 37 +HLA-A*29:02 2 14 22 9 LHAQLHPHE 23637.63 37 +HLA-A*29:02 4 3 11 9 WPESSLPFR 23668.08 37 +HLA-A*29:02 5 3 11 9 WPESSLPFR 23668.08 37 +HLA-A*29:02 2 10 18 9 QKTPLHAQL 25449.21 42 +HLA-A*29:02 4 9 17 9 PFRKLHCTR 25530.30 42 +HLA-A*29:02 5 9 17 9 PFRKLHCTR 25530.30 42 +HLA-A*29:02 2 39 47 9 RRLLQLLLQ 25883.82 43 +HLA-A*29:02 2 37 45 9 EGRRLLQLL 27215.87 47 +HLA-A*29:02 2 8 16 9 SIQKTPLHA 27316.47 47 +HLA-A*29:02 1 3 11 9 GFEDSVRKS 27354.62 47 +HLA-A*29:02 5 37 45 9 VKDVVFYNS 27386.30 47 +HLA-A*29:02 3 7 15 9 HFHSENSTA 27799.49 49 +HLA-A*29:02 2 9 17 9 IQKTPLHAQ 27827.78 49 +HLA-A*29:02 2 21 29 9 HELVCFFHP 27883.54 49 +HLA-A*29:02 4 5 13 9 ESSLPFRKL 27992.35 50 +HLA-A*29:02 5 5 13 9 ESSLPFRKL 27992.35 50 +HLA-A*29:02 3 5 13 9 NLHFHSENS 28405.47 51 +HLA-A*29:02 2 4 12 9 RIFTSIQKT 28568.83 52 +HLA-A*29:02 1 2 10 9 TGFEDSVRK 28705.46 52 +HLA-A*29:02 3 13 21 9 STARATTST 28722.86 52 +HLA-A*29:02 2 36 44 9 GEGRRLLQL 29248.48 54 +HLA-A*29:02 5 43 51 9 YNSYSKRPD 29248.78 54 +HLA-A*29:02 2 2 10 9 LARIFTSIQ 29477.21 55 +HLA-A*29:02 5 54 62 9 NGWMSYLSE 29658.61 55 +HLA-A*29:02 3 6 14 9 LHFHSENST 29941.06 56 +HLA-A*29:02 3 4 12 9 PNLHFHSEN 30313.63 58 +HLA-A*29:02 5 46 54 9 YSKRPDNEN 30354.99 58 +HLA-A*29:02 2 3 11 9 ARIFTSIQK 30561.94 59 +HLA-A*29:02 2 35 43 9 TGEGRRLLQ 30972.07 61 +HLA-A*29:02 4 4 12 9 PESSLPFRK 31208.20 61 +HLA-A*29:02 5 4 12 9 PESSLPFRK 31208.20 61 +HLA-A*29:02 5 14 22 9 HCTRNYIHM 31253.16 62 +HLA-A*29:02 5 31 39 9 RTLAVLVKD 31887.80 64 +HLA-A*29:02 4 7 15 9 SLPFRKLHC 32047.60 65 +HLA-A*29:02 5 7 15 9 SLPFRKLHC 32047.60 65 +HLA-A*29:02 1 7 15 9 SVRKSSIPK 32310.45 66 +HLA-A*29:02 5 44 52 9 NSYSKRPDN 32385.00 66 +HLA-A*29:02 2 12 20 9 TPLHAQLHP 32581.12 67 +HLA-A*29:02 1 1 9 9 ITGFEDSVR 32640.39 67 +HLA-A*29:02 3 3 11 9 GPNLHFHSE 32653.11 67 +HLA-A*29:02 2 17 25 9 QLHPHELVC 33029.76 69 +HLA-A*29:02 5 30 38 9 LRTLAVLVK 33062.67 69 +HLA-A*29:02 3 9 17 9 HSENSTARA 33539.71 71 +HLA-A*29:02 4 8 16 9 LPFRKLHCT 33598.18 71 +HLA-A*29:02 5 8 16 9 LPFRKLHCT 33598.18 71 +HLA-A*29:02 3 12 20 9 NSTARATTS 33755.58 72 +HLA-A*29:02 5 45 53 9 SYSKRPDNE 33779.34 72 +HLA-A*29:02 2 27 35 9 FHPENPGCT 34960.66 76 +HLA-A*29:02 2 30 38 9 ENPGCTGEG 35131.69 76 +HLA-A*29:02 4 1 9 9 APWPESSLP 35259.25 77 +HLA-A*29:02 5 1 9 9 APWPESSLP 35259.25 77 +HLA-A*29:02 2 31 39 9 NPGCTGEGR 35523.10 78 +HLA-A*29:02 4 10 18 9 FRKLHCTRN 35593.11 78 +HLA-A*29:02 5 10 18 9 FRKLHCTRN 35593.11 78 +HLA-A*29:02 2 24 32 9 VCFFHPENP 35646.29 78 +HLA-A*29:02 5 33 41 9 LAVLVKDVV 35679.87 78 +HLA-A*29:02 3 2 10 9 PGPNLHFHS 35758.72 78 +HLA-A*29:02 5 49 57 9 RPDNENGWM 36016.54 79 +HLA-A*29:02 5 50 58 9 PDNENGWMS 36173.53 79 +HLA-A*29:02 1 4 12 9 FEDSVRKSS 36907.69 83 +HLA-A*29:02 3 11 19 9 ENSTARATT 36936.45 83 +HLA-A*29:02 1 9 17 9 RKSSIPKNV 37337.88 85 +HLA-A*29:02 3 10 18 9 SENSTARAT 38042.53 88 +HLA-A*29:02 2 33 41 9 GCTGEGRRL 38555.95 90 +HLA-A*29:02 2 29 37 9 PENPGCTGE 38861.25 91 +HLA-A*29:02 1 5 13 9 EDSVRKSSI 39014.61 92 +HLA-A*29:02 5 48 56 9 KRPDNENGW 39757.80 94 +HLA-A*29:02 1 8 16 9 VRKSSIPKN 40002.45 95 +HLA-A*29:02 2 32 40 9 PGCTGEGRR 41335.19 99 +HLA-A*29:02 2 28 36 9 HPENPGCTG 41340.55 99 +HLA-A*29:02 5 47 55 9 SKRPDNENG 42436.38 100 +HLA-A*29:02 1 6 14 9 DSVRKSSIP 43503.33 100 diff --git a/tests/test_pvacseq.py b/tests/test_pvacseq.py index 64e5196..7dc3c61 100644 --- a/tests/test_pvacseq.py +++ b/tests/test_pvacseq.py @@ -47,13 +47,8 @@ def make_response(data, files, path): reader.close() return response_obj -def generate_class_i_call(method, allele, length, path, input_path): - reader = open(os.path.join( - input_path, - "MHC_Class_I", - "tmp", - "Test_21.fa.split_1-48" - ), mode='r') +def generate_class_i_call(method, allele, length, input_file): + reader = open(input_file, mode='r') text = reader.read() reader.close() return unittest.mock.call('http://tools-cluster-interface.iedb.org/tools_api/mhci/', data={ @@ -177,6 +172,8 @@ def test_pvacseq_pipeline(self): '--tdna-vaf', '20', '-d', 'full', ]) + self.assertEqual(len(self.request_mock.mock_calls), 8) + pvacseq.lib.main.main([ os.path.join(self.test_data_directory, "input.vcf"), 'Test', @@ -188,6 +185,7 @@ def test_pvacseq_pipeline(self): '--keep-tmp-files', '-d', 'full', ]) + self.assertEqual(len(self.request_mock.mock_calls), 9) for file_name in ( 'Test.tsv', @@ -227,14 +225,13 @@ def test_pvacseq_pipeline(self): output_file = os.path.join(output_dir.name, 'MHC_Class_I', 'log', file_name) self.assertTrue(os.path.exists(output_file)) - self.assertEqual(len(self.request_mock.mock_calls), 9) #Class I output files methods = self.methods for method in methods.keys(): for allele in methods[method].keys(): for length in methods[method][allele]: self.request_mock.assert_has_calls([ - generate_class_i_call(method, allele, length, self.test_data_directory, output_dir.name) + generate_class_i_call(method, allele, length, os.path.join(output_dir.name, "MHC_Class_I", "tmp", "Test_21.fa.split_1-48")) ]) output_file = os.path.join(output_dir.name, "MHC_Class_I", "tmp", 'Test.%s.%s.%s.tsv_1-48' % (method, allele, length)) expected_file = os.path.join(self.test_data_directory, "MHC_Class_I", "tmp", 'Test.%s.%s.%s.tsv_1-48' % (method, allele, length)) @@ -350,3 +347,48 @@ def test_pvacseq_pipeline_sleep(self): self.assertTrue(duration_1 > duration_2) + def test_pvacseq_pipeline_for_fusions(self): + pvac_script_path = os.path.join( + self.pVac_directory, + 'pvacseq', + "pvacseq.py" + ) + output_dir = tempfile.TemporaryDirectory(dir = self.test_data_directory) + + pvacseq.lib.main.main([ + os.path.join(self.test_data_directory, "fusions_annotated.bedpe"), + 'Test', + 'HLA-A*29:02', + 'NetMHC', + output_dir.name, + '-e', '9', + '--top-score-metric=lowest', + '--keep-tmp-files', + ]) + + for file_name in ( + 'Test.tsv', + 'Test.tsv_1-5', + 'Test.combined.parsed.tsv', + 'Test.filtered.binding.tsv', + 'Test.final.tsv', + ): + output_file = os.path.join(output_dir.name, 'MHC_Class_I', file_name) + expected_file = os.path.join(self.test_data_directory, 'fusions', 'MHC_Class_I', file_name) + self.assertTrue(compare(output_file, expected_file)) + + for file_name in ( + 'Test_21.fa.split_1-10', + 'Test_21.fa.split_1-10.key', + 'Test.ann.HLA-A*29:02.9.tsv_1-10', + 'Test.HLA-A*29:02.9.parsed.tsv_1-10', + ): + output_file = os.path.join(output_dir.name, 'MHC_Class_I', 'tmp', file_name) + expected_file = os.path.join(self.test_data_directory, 'fusions', 'MHC_Class_I', 'tmp', file_name) + self.assertTrue(compare(output_file, expected_file)) + + self.request_mock.assert_has_calls([ + generate_class_i_call('ann', 'HLA-A*29:02', 9, os.path.join(output_dir.name, "MHC_Class_I", "tmp", "Test_21.fa.split_1-10")) + ]) + + output_dir.cleanup()