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Update example data
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@susannasiebert
susannasiebert committed Jan 16, 2025
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Showing 24 changed files with 55,119 additions and 19,239 deletions.
22 changes: 11 additions & 11 deletions pvactools/tools/pvacbind/example_data/results/MHC_Class_I/Test.all_epitopes.aggregated.tsv
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Expand Up @@ -36,14 +36,14 @@ ID A*02:01 B*35:01 Best Peptide Prob Pos Num Included Peptides Num Passing Pepti
27 1 SLLHTVSPEP None 1 0 3556.960 7.400 Poor Pending
35 2 NPETDYLTG None 2 0 3595.485 6.200 Poor Pending
20 1 DLIGKHGGV None 1 0 4145.685 12.500 Poor Pending
39 TSAKTTVVV None 0 0 5514.896 15.500 Poor Pending
40 TSAKTTVVV None 0 0 5514.896 15.500 Poor Pending
13 IANEDAAQG None 0 0 5541.375 8.587 Poor Pending
14 IANQDAAQG None 0 0 5738.350 12.249 Poor Pending
46 YESRVEPPH None 0 0 6159.300 13.850 Poor Pending
29 SAGQHWARL None 0 0 7663.630 12.785 Poor Pending
45 EASGSESRV None 0 0 10173.480 19.000 Poor Pending
8 SGGSHVWTH None 0 0 10761.968 23.096 Poor Pending
22 SPVKEEEKT None 0 0 12628.540 13.580 Poor Pending
21 SPVKEEEK None 0 0 14657.070 17.153 Poor Pending
7 WTRSRDPEG None 0 0 20800.365 35.287 Poor Pending
39 1 TSAKTTVVV None 1 0 5514.896 15.500 Poor Pending
40 1 TSAKTTVVV None 1 0 5514.896 15.500 Poor Pending
13 1 IANEDAAQG None 1 0 5541.375 8.587 Poor Pending
14 1 IANQDAAQG None 1 0 5738.350 12.249 Poor Pending
46 1 YESRVEPPH None 1 0 6159.300 13.850 Poor Pending
29 1 SAGQHWARL None 1 0 7663.630 12.785 Poor Pending
45 1 EASGSESRV None 1 0 10173.480 19.000 Poor Pending
8 1 SGGSHVWTH None 1 0 10761.968 23.096 Poor Pending
22 1 SPVKEEEKT None 1 0 12628.540 13.580 Poor Pending
21 1 SPVKEEEK None 1 0 14657.070 17.153 Poor Pending
7 1 WTRSRDPEG None 1 0 20800.365 35.287 Poor Pending
24 changes: 12 additions & 12 deletions pvactools/tools/pvacbind/example_data/results/MHC_Class_II/Test.all_epitopes.aggregated.tsv
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Expand Up @@ -35,15 +35,15 @@ ID DRB1*11:01 Best Peptide Prob Pos Num Included Peptides Num Passing Peptides I
35 1 AIAGTLKFNPETDYL None 1 0 3844.535 65.000 Poor Pending
31 1 DDMDCLSDRCKILQV None 1 0 3900.880 64.000 Poor Pending
24 1 SLMVCELAGNLFNCE None 1 0 4781.440 70.000 Poor Pending
23 SLMVCELAGNPFNCE None 0 0 5518.185 74.000 Poor Pending
14 AVQGIANQDAAQGIA None 0 0 6113.120 70.000 Poor Pending
8 GGSHVWTHSRDPEGS None 0 0 6831.935 71.000 Poor Pending
4 SAAAAAAAVIPTVST None 0 0 6950.420 82.000 Poor Pending
3 AAAAAAAAVIPTVST None 0 0 7066.755 82.000 Poor Pending
27 SLLHTVSPEPPRPPQ None 0 0 7421.920 69.000 Poor Pending
12 NKSVNEALNNLLTEE None 0 0 7705.835 67.000 Poor Pending
13 AVQGIANEDAAQGIA None 0 0 8697.355 79.000 Poor Pending
22 EEEKTQEVKVKEPPK None 0 0 12127.835 86.410 Poor Pending
46 EASGYESRVEPPHEN None 0 0 14269.785 86.000 Poor Pending
21 EEEKPQEVKVKEPPK None 0 0 15116.485 83.650 Poor Pending
45 AREERTEASGSESRV None 0 0 25985.790 96.000 Poor Pending
23 1 SLMVCELAGNPFNCE None 1 0 5518.185 74.000 Poor Pending
14 1 AVQGIANQDAAQGIA None 1 0 6113.120 70.000 Poor Pending
8 1 GGSHVWTHSRDPEGS None 1 0 6831.935 71.000 Poor Pending
4 1 SAAAAAAAVIPTVST None 1 0 6950.420 82.000 Poor Pending
3 1 AAAAAAAAVIPTVST None 1 0 7066.755 82.000 Poor Pending
27 1 SLLHTVSPEPPRPPQ None 1 0 7421.920 69.000 Poor Pending
12 1 NKSVNEALNNLLTEE None 1 0 7705.835 67.000 Poor Pending
13 1 AVQGIANEDAAQGIA None 1 0 8697.355 79.000 Poor Pending
22 1 EEEKTQEVKVKEPPK None 1 0 12127.835 86.410 Poor Pending
46 1 EASGYESRVEPPHEN None 1 0 14269.785 86.000 Poor Pending
21 1 EEEKPQEVKVKEPPK None 1 0 15116.485 83.650 Poor Pending
45 1 AREERTEASGSESRV None 1 0 25985.790 96.000 Poor Pending
14 changes: 7 additions & 7 deletions pvactools/tools/pvacbind/example_data/results/combined/Test.all_epitopes.aggregated.tsv
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Expand Up @@ -40,10 +40,10 @@ ID DRB1*11:01 A*02:01 B*35:01 Best Peptide Prob Pos Num Included Peptides Num Pa
36 4 1 AIAGTLKFNPQTDYL None 5 0 2466.625 57.000 Poor Pending
27 1 SLLHTVSPEP None 1 0 3556.960 7.400 Poor Pending
35 1 2 NPETDYLTG None 3 0 3595.485 6.200 Poor Pending
13 IANEDAAQG None 0 0 5541.375 8.587 Poor Pending
14 IANQDAAQG None 0 0 5738.350 12.249 Poor Pending
46 YESRVEPPH None 0 0 6159.300 13.850 Poor Pending
8 GGSHVWTHSRDPEGS None 0 0 6831.935 71.000 Poor Pending
45 EASGSESRV None 0 0 10173.480 19.000 Poor Pending
22 EEEKTQEVKVKEPPK None 0 0 12127.835 86.410 Poor Pending
21 SPVKEEEK None 0 0 14657.070 17.153 Poor Pending
13 1 IANEDAAQG None 1 0 5541.375 8.587 Poor Pending
14 1 IANQDAAQG None 1 0 5738.350 12.249 Poor Pending
46 1 YESRVEPPH None 1 0 6159.300 13.850 Poor Pending
8 1 GGSHVWTHSRDPEGS None 1 0 6831.935 71.000 Poor Pending
45 1 EASGSESRV None 1 0 10173.480 19.000 Poor Pending
22 1 EEEKTQEVKVKEPPK None 1 0 12127.835 86.410 Poor Pending
21 1 SPVKEEEK None 1 0 14657.070 17.153 Poor Pending
24 changes: 12 additions & 12 deletions ...tools/pvacfuse/example_data/agfusion_results/MHC_Class_I/Test.all_epitopes.aggregated.tsv
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Expand Up @@ -22,15 +22,15 @@ ID A*02:01 B*35:01 Gene Best Peptide Best Transcript Allele Prob Pos Num Include
11.DNAJC7-CDK17.ENST00000457167-ENST00000261211.frameshift_fusion.25 1 1 DNAJC7-CDK17 LDDQEAKSF ENST00000457167-ENST00000261211 HLA-B*35:01 None 2 0 4488.075 14.000 NA NA Poor Pending
12.DNAJC7-CDK17.ENST00000457167-ENST00000261211.frameshift_fusion.25 1 1 DNAJC7-CDK17 LDDQEAKSF ENST00000457167-ENST00000261211 HLA-B*35:01 None 2 0 4488.075 14.000 NA NA Poor Pending
32.TIMP3-COL3A1.ENST00000266085-ENST00000304636.frameshift_fusion.211 1 TIMP3-COL3A1 NATDPGPEA ENST00000266085-ENST00000304636 HLA-B*35:01 None 1 0 4879.470 6.360 NA NA Poor Pending
36.TTC26-NDUFV2.ENST00000464848-ENST00000318388.inframe_fusion.239 TTC26-NDUFV2 RLYNGRAAEG ENST00000464848-ENST00000318388 HLA-A*02:01 None 0 0 5495.235 9.400 NA NA Poor Pending
5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 CEP192-TMEM260 DPEACEESV ENST00000506447-ENST00000261556 HLA-B*35:01 None 0 0 5935.036 8.900 NA NA Poor Pending
15.LCORL-GNAS.ENST00000382226-ENST00000371100.inframe_fusion.143 LCORL-GNAS ALFRKKGA ENST00000382226-ENST00000371100 HLA-A*02:01 None 0 0 6647.795 23.226 NA NA Poor Pending
6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 CLEC16A-RMI2 CVQTDEEKV ENST00000409790-ENST00000312499 HLA-A*02:01 None 0 0 7223.131 19.000 NA NA Poor Pending
38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 TUB-RIC3 APASAKRTK ENST00000305253-ENST00000309737 HLA-B*35:01 None 0 0 7902.902 19.000 NA NA Poor Pending
37.TTC39B-C6orf62.ENST00000512701-ENST00000378119.inframe_fusion.465 TTC39B-C6orf62 KWSKAKFEF ENST00000512701-ENST00000378119 HLA-B*35:01 None 0 0 8453.905 15.000 NA NA Poor Pending
17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 MAX-TMEM260 VPSLQGEKG ENST00000358664-ENST00000261556 HLA-B*35:01 None 0 0 12601.620 12.000 NA NA Poor Pending
21.PHTF1-YARS.ENST00000369604-ENST00000373477.inframe_fusion.15 PHTF1-YARS YQKKESKIDL ENST00000369604-ENST00000373477 HLA-A*02:01 None 0 0 13729.865 28.000 NA NA Poor Pending
41.ZC3H11A-KLHL12.ENST00000545588-ENST00000367261.frameshift_fusion.291 ZC3H11A-KLHL12 RLGKRKFSAG ENST00000545588-ENST00000367261 HLA-A*02:01 None 0 0 15600.145 33.268 NA NA Poor Pending
19.MIPOL1-PGAP1.ENST00000327441-ENST00000354764.frameshift_fusion.6 MIPOL1-PGAP1 NWSKVCCRL ENST00000327441-ENST00000354764 HLA-A*02:01 None 0 0 16894.461 34.000 NA NA Poor Pending
28.SNRPB2-METTL18.ENST00000246071-ENST00000310392.frameshift_fusion.215 SNRPB2-METTL18 QGFKITPSQ ENST00000246071-ENST00000310392 HLA-B*35:01 None 0 0 21917.167 36.000 NA NA Poor Pending
4.CDC37L1-BTG3.ENST00000381854-ENST00000339775.frameshift_fusion.169 CDC37L1-BTG3 KIRHFDEE ENST00000381854-ENST00000339775 HLA-A*02:01 None 0 0 35010.660 71.000 NA NA Poor Pending
36.TTC26-NDUFV2.ENST00000464848-ENST00000318388.inframe_fusion.239 1 TTC26-NDUFV2 RLYNGRAAEG ENST00000464848-ENST00000318388 HLA-A*02:01 None 1 0 5495.235 9.400 NA NA Poor Pending
5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 1 CEP192-TMEM260 DPEACEESV ENST00000506447-ENST00000261556 HLA-B*35:01 None 1 0 5935.036 8.900 NA NA Poor Pending
15.LCORL-GNAS.ENST00000382226-ENST00000371100.inframe_fusion.143 1 LCORL-GNAS ALFRKKGA ENST00000382226-ENST00000371100 HLA-A*02:01 None 1 0 6647.795 23.226 NA NA Poor Pending
6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 1 CLEC16A-RMI2 CVQTDEEKV ENST00000409790-ENST00000312499 HLA-A*02:01 None 1 0 7223.131 19.000 NA NA Poor Pending
38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 1 TUB-RIC3 APASAKRTK ENST00000305253-ENST00000309737 HLA-B*35:01 None 1 0 7902.902 19.000 NA NA Poor Pending
37.TTC39B-C6orf62.ENST00000512701-ENST00000378119.inframe_fusion.465 1 TTC39B-C6orf62 KWSKAKFEF ENST00000512701-ENST00000378119 HLA-B*35:01 None 1 0 8453.905 15.000 NA NA Poor Pending
17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 1 MAX-TMEM260 VPSLQGEKG ENST00000358664-ENST00000261556 HLA-B*35:01 None 1 0 12601.620 12.000 NA NA Poor Pending
21.PHTF1-YARS.ENST00000369604-ENST00000373477.inframe_fusion.15 1 PHTF1-YARS YQKKESKIDL ENST00000369604-ENST00000373477 HLA-A*02:01 None 1 0 13729.865 28.000 NA NA Poor Pending
41.ZC3H11A-KLHL12.ENST00000545588-ENST00000367261.frameshift_fusion.291 1 ZC3H11A-KLHL12 RLGKRKFSAG ENST00000545588-ENST00000367261 HLA-A*02:01 None 1 0 15600.145 33.268 NA NA Poor Pending
19.MIPOL1-PGAP1.ENST00000327441-ENST00000354764.frameshift_fusion.6 1 MIPOL1-PGAP1 NWSKVCCRL ENST00000327441-ENST00000354764 HLA-A*02:01 None 1 0 16894.461 34.000 NA NA Poor Pending
28.SNRPB2-METTL18.ENST00000246071-ENST00000310392.frameshift_fusion.215 1 SNRPB2-METTL18 QGFKITPSQ ENST00000246071-ENST00000310392 HLA-B*35:01 None 1 0 21917.167 36.000 NA NA Poor Pending
4.CDC37L1-BTG3.ENST00000381854-ENST00000339775.frameshift_fusion.169 1 CDC37L1-BTG3 KIRHFDEE ENST00000381854-ENST00000339775 HLA-A*02:01 None 1 0 35010.660 71.000 NA NA Poor Pending
10 changes: 5 additions & 5 deletions ...ools/pvacfuse/example_data/agfusion_results/MHC_Class_II/Test.all_epitopes.aggregated.tsv
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Expand Up @@ -28,8 +28,8 @@ ID DRB1*11:01 Gene Best Peptide Best Transcript Allele Prob Pos Num Included Pep
29.TAOK3-MARCH1.ENST00000392533-ENST00000503008.frameshift_fusion.214 4 TAOK3-MARCH1 KVDIWSLGITCIELV ENST00000392533-ENST00000503008 DRB1*11:01 None 4 0 2887.565 61.000 NA NA Poor Pending
3.BTBD8-ELAVL4.ENST00000342818-ENST00000357083.frameshift_fusion.181 2 BTBD8-ELAVL4 DDDFISNGSPQLPLM ENST00000342818-ENST00000357083 DRB1*11:01 None 2 0 3275.675 44.690 NA NA Poor Pending
27.SMG1-PHF20.ENST00000446231-ENST00000374012.frameshift_fusion.3540 1 SMG1-PHF20 ATYQPSFAADDKAST ENST00000446231-ENST00000374012 DRB1*11:01 None 1 0 3853.640 45.070 NA NA Poor Pending
38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 TUB-RIC3 TRPTAPASAKRTKAA ENST00000305253-ENST00000309737 DRB1*11:01 None 0 0 5064.720 69.000 NA NA Poor Pending
17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 MAX-TMEM260 HSLRDSVPSLQGEKG ENST00000358664-ENST00000261556 DRB1*11:01 None 0 0 5813.705 57.000 NA NA Poor Pending
5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 CEP192-TMEM260 ESVCDQRTNYVIDKF ENST00000506447-ENST00000261556 DRB1*11:01 None 0 0 7719.265 81.000 NA NA Poor Pending
32.TIMP3-COL3A1.ENST00000266085-ENST00000304636.frameshift_fusion.211 TIMP3-COL3A1 PDKSIINATDPGPEA ENST00000266085-ENST00000304636 DRB1*11:01 None 0 0 13347.750 90.000 NA NA Poor Pending
6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 CLEC16A-RMI2 SHVIELDDCVQTDEE ENST00000409790-ENST00000312499 DRB1*11:01 None 0 0 14800.050 90.000 NA NA Poor Pending
38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 1 TUB-RIC3 TRPTAPASAKRTKAA ENST00000305253-ENST00000309737 DRB1*11:01 None 1 0 5064.720 69.000 NA NA Poor Pending
17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 1 MAX-TMEM260 HSLRDSVPSLQGEKG ENST00000358664-ENST00000261556 DRB1*11:01 None 1 0 5813.705 57.000 NA NA Poor Pending
5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 1 CEP192-TMEM260 ESVCDQRTNYVIDKF ENST00000506447-ENST00000261556 DRB1*11:01 None 1 0 7719.265 81.000 NA NA Poor Pending
32.TIMP3-COL3A1.ENST00000266085-ENST00000304636.frameshift_fusion.211 1 TIMP3-COL3A1 PDKSIINATDPGPEA ENST00000266085-ENST00000304636 DRB1*11:01 None 1 0 13347.750 90.000 NA NA Poor Pending
6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 1 CLEC16A-RMI2 SHVIELDDCVQTDEE ENST00000409790-ENST00000312499 DRB1*11:01 None 1 0 14800.050 90.000 NA NA Poor Pending
10 changes: 5 additions & 5 deletions ...ls/tools/pvacfuse/example_data/agfusion_results/combined/Test.all_epitopes.aggregated.tsv
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Expand Up @@ -29,8 +29,8 @@ ID DRB1*11:01 A*02:01 B*35:01 Gene Best Peptide Best Transcript Allele Prob Pos
35.TRAPPC9-NUP50.ENST00000389328-ENST00000347635.frameshift_fusion.1034 8 2 1 TRAPPC9-NUP50 FSCCKWPYHL ENST00000389328-ENST00000347635 HLA-A*02:01 None 11 0 2130.755 6.400 NA NA Poor Pending
27.SMG1-PHF20.ENST00000446231-ENST00000374012.frameshift_fusion.3540 1 1 SMG1-PHF20 FAADDKAST ENST00000446231-ENST00000374012 HLA-B*35:01 None 2 0 2614.100 2.900 NA NA Poor Pending
32.TIMP3-COL3A1.ENST00000266085-ENST00000304636.frameshift_fusion.211 1 TIMP3-COL3A1 NATDPGPEA ENST00000266085-ENST00000304636 HLA-B*35:01 None 1 0 4879.470 6.360 NA NA Poor Pending
38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 TUB-RIC3 TRPTAPASAKRTKAA ENST00000305253-ENST00000309737 DRB1*11:01 None 0 0 5064.720 69.000 NA NA Poor Pending
17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 MAX-TMEM260 HSLRDSVPSLQGEKG ENST00000358664-ENST00000261556 DRB1*11:01 None 0 0 5813.705 57.000 NA NA Poor Pending
5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 CEP192-TMEM260 DPEACEESV ENST00000506447-ENST00000261556 HLA-B*35:01 None 0 0 5935.036 8.900 NA NA Poor Pending
6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 CLEC16A-RMI2 CVQTDEEKV ENST00000409790-ENST00000312499 HLA-A*02:01 None 0 0 7223.131 19.000 NA NA Poor Pending
19.MIPOL1-PGAP1.ENST00000327441-ENST00000354764.frameshift_fusion.6 MIPOL1-PGAP1 NWSKVCCRL ENST00000327441-ENST00000354764 HLA-A*02:01 None 0 0 16894.461 34.000 NA NA Poor Pending
38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 1 TUB-RIC3 TRPTAPASAKRTKAA ENST00000305253-ENST00000309737 DRB1*11:01 None 1 0 5064.720 69.000 NA NA Poor Pending
17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 1 MAX-TMEM260 HSLRDSVPSLQGEKG ENST00000358664-ENST00000261556 DRB1*11:01 None 1 0 5813.705 57.000 NA NA Poor Pending
5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 1 CEP192-TMEM260 DPEACEESV ENST00000506447-ENST00000261556 HLA-B*35:01 None 1 0 5935.036 8.900 NA NA Poor Pending
6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 1 CLEC16A-RMI2 CVQTDEEKV ENST00000409790-ENST00000312499 HLA-A*02:01 None 1 0 7223.131 19.000 NA NA Poor Pending
19.MIPOL1-PGAP1.ENST00000327441-ENST00000354764.frameshift_fusion.6 1 MIPOL1-PGAP1 NWSKVCCRL ENST00000327441-ENST00000354764 HLA-A*02:01 None 1 0 16894.461 34.000 NA NA Poor Pending
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