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Update import/export test study to new fixes
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Diff for: ‎test/test_data/study_es_0_import_export/data_generic_assay_limit-value_mutational_signature.txt

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ENTITY_STABLE_ID confidenceStatement description name TCGA-A1-A0SB-01 TCGA-A1-A0SD-01 TCGA-A1-A0SE-01 TCGA-A1-A0SH-01 TCGA-A2-A04U-01 TCGA-B6-A0RS-01 TCGA-BH-A0HP-01 TCGA-BH-A18P-01
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mean_1 0.370266873 0.010373016 0.005419294 0.022753384 0.037687823 0.016708976 0.100042446 0.104214723
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mean_1 Signature 1, the aging signature, is detected in this case. mean_1 mean_1 0.370266873 0.010373016 0.005419294 0.022753384 0.037687823 0.016708976 0.100042446 0.104214723
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mean_10 Signature 10, the POLE signature, is detected in this case. It is associated with functions to the exonucleus domain of the POLE gene and enormous mutational burden. Oftentimes MMR signatures 6, 14,16, 20,21 and 26 co-occur with the POLE signature. mean_10 mean_10 0.002709404 0.009212318 0.002650657 0.005475484 0.074175715 0.033049207 0.027323826 0.008861145
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mean_11 Signature 11, the Temozolomide (TMZ) signature, is detected in this case. mean_11 mean_11 0.006035782 0.010095773 0.011926486 0.010637541 0.012168938 0.006641113 0.025730547 0.020463421
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mean_12 Signature 12 is detected in this case. We are not confident that we are able to detect signature 9 in the IMPACT cohort. In the literature it is found in liver cancer. mean_12 mean_12 0.026432791 0.012953054 0.002587003 0.02225923 0.031026708 0.01642898 0.022392184 0.013437576

Diff for: ‎test/test_data/study_es_0_import_export/data_generic_assay_limit-value_treatment_ec50.txt

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ENTITY_STABLE_ID DESCRIPTION NAME URL TCGA-A1-A0SB-01 TCGA-A1-A0SD-01 TCGA-A1-A0SE-01 TCGA-A1-A0SH-01 TCGA-A2-A04U-01 TCGA-B6-A0RS-01 TCGA-BH-A0HP-01 TCGA-BH-A18P-01
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17-AAG 0.22807844 0.329701692 0.053038094 0.07082279 0.150094494 0.422571242 0.1517988 0.279530227
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17-AAG Desc of 17-AAG Name of 17-AAG Url of 17-AAG 0.22807844 0.329701692 0.053038094 0.07082279 0.150094494 0.422571242 0.1517988 0.279530227
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AEW541 Desc of AEW541 Name of AEW541 Url of AEW541 > 8 2.329924107 2.68212986 5.002314091 1.736181378 4.260821819 > 8 7.613147736
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AZD0530 Desc of AZD0530 Name of AZD0530 Url of AZD0530 > 8 > 8 4.597949505 3.192236662 > 8 7.261883259 1.071310043 > 8
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AZD6244 Desc of AZD6244 Name of AZD6244 Url of AZD6244 > 8 > 8 > 8 > 8 > 8 > 8 > 8 > 8
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Erlotinib Desc of Erlotinib Name of Erlotinib Url of Erlotinib > 8 > 8 > 8 2.439512491 > 8 4.232964516 2.325097322 > 8
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Irinotecan Desc of Irinotecan Name of Irinotecan Url of Irinotecan NA 0.080764666 NA 0.06704437 0.069568723 0.034992039 0.740817904 0.209220141
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L-685458 Desc of L-685458 Name of L-685458 Url of L-685458 > 8 > 8 3.267752409 > 8 > 8 0.332892686 > 8 > 8
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Lapatinib Desc of Lapatinib Name of Lapatinib Url of Lapatinib > 8 7.847305298 > 8 2.30776763 > 8 0.849476227 1.057461143 7.178035259
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Nilotinib NA > 8 NA 7.475354671 > 8 1.910434365 > 8 > 8
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LBW242 Desc of LBW242 Name of LBW242 Url of LBW242 > 8 > 8 > 8 > 8 > 8 > 8 > 8 > 8
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Nilotinib Desc of Nilotinib Name of Nilotinib Url of Nilotinib NA > 8 NA 7.475354671 > 8 1.910434365 > 8 > 8

Diff for: ‎test/test_data/study_es_0_import_export/data_generic_assay_limit-value_treatment_ic50.txt

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ENTITY_STABLE_ID DESCRIPTION NAME URL TCGA-A1-A0SB-01 TCGA-A1-A0SD-01 TCGA-A1-A0SE-01 TCGA-A1-A0SH-01 TCGA-A2-A04U-01 TCGA-B6-A0RS-01 TCGA-BH-A0HP-01 TCGA-BH-A18P-01
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17-AAG 0.22807844 0.329701692 0.053038094 0.07082279 0.150094494 0.422571242 0.1517988 0.279530227
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17-AAG Desc of 17-AAG Name of 17-AAG Url of 17-AAG 0.22807844 0.329701692 0.053038094 0.07082279 0.150094494 0.422571242 0.1517988 0.279530227
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AEW541 Desc of AEW541 Name of AEW541 Url of AEW541 >8 2.329924107 2.68212986 5.002314091 1.736181378 4.260821819 >8 7.613147736
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AZD0530 Desc of AZD0530 Name of AZD0530 Url of AZD0530 >8 >8 4.597949505 3.192236662 >8 7.261883259 0.123 >8
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AZD6244 Desc of AZD6244 Name of AZD6244 Url of AZD6244 >8 >8 >8 >8 >8 >8 >8 >8
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Erlotinib Desc of Erlotinib Name of Erlotinib Url of Erlotinib >8 >8 >8 2.439512491 >8 4.232964516 2.325097322 >8
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Irinotecan Desc of Irinotecan Name of Irinotecan Url of Irinotecan NA 0.080764666 NA 0.06704437 0.069568723 0.034992039 0.740817904 0.209220141
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L-685458 Desc of L-685458 Name of L-685458 Url of L-685458 >8 >8 3.267752409 >8 >8 0.332892686 >8 >8
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Lapatinib Desc of Lapatinib Name of Lapatinib Url of Lapatinib >8 7.847305298 >8 2.30776763 >8 0.849476227 1.057461143 7.178035259
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Nilotinib NA >8 NA 7.475354671 >8 1.910434365 >8 >8
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LBW242 Desc of LBW242 Name of LBW242 Url of LBW242 >8 >8 >8 >8 >8 >8 >8 >8
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Nilotinib Desc of Nilotinib Name of Nilotinib Url of Nilotinib NA >8 NA 7.475354671 >8 1.910434365 >8 >8

Diff for: ‎test/test_data/study_es_0_import_export/data_mutation_extended_maf_mutations.txt

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Original file line numberDiff line numberDiff line change
@@ -27,8 +27,8 @@ DTNB 1838 genome.wustl.edu GRCh37 2 25678299 25678299 + Missense_Mutation SNP C
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ABLIM1 3983 genome.wustl.edu GRCh37 10 116247760 116247760 + Missense_Mutation SNP T C C NA NA TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 T T NA NA NA NA Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx
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MSH3 4437 genome.wustl.edu GRCh37 5 80024722 80024722 + Frame_Shift_Del DEL T - - NA NA TCGA-A1-A0SB-02 TCGA-A1-A0SB-10 T T NA NA NA NA Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx
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MYB 4602 genome.wustl.edu GRCh37 6 135507043 135507044 + Frame_Shift_Ins INS - A A NA NA TCGA-A1-A0SB-02 TCGA-A1-A0SB-10 - - NA NA NA NA Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx
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TP53 7157 genome.wustl.edu GRCh37 17 7576851 7576851 + Splice_Site SNP A C C NA NA TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 A A NA NA NA NA Unknown NA Somatic Phase_IV Capture NA 1 dbGAP Illumina GAIIx
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TP53 7157 genome.wustl.edu GRCh37 17 7578253 7578253 + Missense_Mutation SNP C A A NA NA TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 A C NA NA NA NA Unknown NA Germline Phase_IV Capture NA 1 dbGAP IlluminaGAIIx
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TP53 7157 genome.wustl.edu GRCh37 17 7576851 7576851 + Splice_Site SNP A C C novel unknown TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 A A NA NA NA NA Unknown NA Somatic Phase_IV Capture NA 1 dbGAP Illumina GAIIx
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PIEZO1 9780 genome.wustl.edu GRCh37 16 88790292 88790292 + Missense_Mutation SNP T C C NA NA TCGA-A1-A0SB-02 TCGA-A1-A0SB-10 T T NA NA NA NA Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx
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ADAMTS20 80070 genome.wustl.edu GRCh37 12 43944926 43944926 + Missense_Mutation SNP T C C NA NA TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 T T NA NA NA NA Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx
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OR11H1 81061 genome.wustl.edu GRCh37 22 16449539 16449539 + Missense_Mutation SNP A G G NA NA TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 A A NA NA NA NA Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx

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