From 1943540b5629e4bb27e372cd883c85f695cda705 Mon Sep 17 00:00:00 2001 From: Ruslan Forostianov Date: Thu, 19 Dec 2024 10:24:17 +0100 Subject: [PATCH] Add git workflow to test study import export --- .github/workflows/integration-test.yml | 5 + test/integration/test_import_export.sh | 25 + .../case_lists/cases_sequenced.txt | 5 + .../data_clinical_samples.txt | 523 ++++++++++++++++++ .../data_mutations.txt | 35 ++ .../meta_clinical_samples.txt | 4 + .../meta_mutations.txt | 8 + .../study_es_0_import_export/meta_study.txt | 9 + 8 files changed, 614 insertions(+) create mode 100755 test/integration/test_import_export.sh create mode 100644 test/test_data/study_es_0_import_export/case_lists/cases_sequenced.txt create mode 100644 test/test_data/study_es_0_import_export/data_clinical_samples.txt create mode 100644 test/test_data/study_es_0_import_export/data_mutations.txt create mode 100644 test/test_data/study_es_0_import_export/meta_clinical_samples.txt create mode 100644 test/test_data/study_es_0_import_export/meta_mutations.txt create mode 100644 test/test_data/study_es_0_import_export/meta_study.txt diff --git a/.github/workflows/integration-test.yml b/.github/workflows/integration-test.yml index a10b74aeefb..7e096414080 100644 --- a/.github/workflows/integration-test.yml +++ b/.github/workflows/integration-test.yml @@ -72,6 +72,11 @@ jobs: working-directory: ./cbioportal-docker-compose run: | $PORTAL_SOURCE_DIR/test/integration/test_load_study.sh + - name: 'TEST - Import and Export of study_es_0_import_export' + if: steps.startup.conclusion == 'success' + working-directory: ./cbioportal-docker-compose + run: | + $PORTAL_SOURCE_DIR/test/integration/test_import_export.sh - name: 'TEST - Add OncoKB annotations to study' if: steps.startup.conclusion == 'success' working-directory: ./cbioportal-docker-compose diff --git a/test/integration/test_import_export.sh b/test/integration/test_import_export.sh new file mode 100755 index 00000000000..861763b9df6 --- /dev/null +++ b/test/integration/test_import_export.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# exit when any of these fails +set -e + +run_in_service() { + service=$1 + shift + docker-compose -f docker-compose.yml -f $PORTAL_SOURCE_DIR/test/integration/docker-compose-localbuild.yml \ + run --rm \ + "$service" bash -c "$@" + return $? # return the exit code of the last command +} + +echo "Importing of the test study with API validation..." +run_in_service cbioportal 'metaImport.py -v -u http://cbioportal-container:8080 -o -s /cbioportal/test/test_data/study_es_0_import_export/' + +echo "Exporting of the test study." +run_in_service cbioportal 'curl -s http://cbioportal-container:8080/export/study/study_es_0_import_export.zip | unzip -d ./output_study_es_0_import_export -' + +echo "Comparing the original and exported studies." +# TODO ignore order of lines in files +run_in_service cbioportal 'diff --recursive /cbioportal/test/test_data/study_es_0_import_export/ ./output_study_es_0_import_export' + +exit 0 diff --git a/test/test_data/study_es_0_import_export/case_lists/cases_sequenced.txt b/test/test_data/study_es_0_import_export/case_lists/cases_sequenced.txt new file mode 100644 index 00000000000..721e3121762 --- /dev/null +++ b/test/test_data/study_es_0_import_export/case_lists/cases_sequenced.txt @@ -0,0 +1,5 @@ +cancer_study_identifier: study_es_0_import_export +stable_id: study_es_0_import_export_sequenced +case_list_name: Samples profiled for mutations +case_list_description: This is this case list that contains all samples that are profiled for mutations. +case_list_ids: TCGA-A2-A04P-01 TCGA-A1-A0SK-01 TCGA-A2-A0CM-01 TCGA-AR-A1AR-01 TCGA-B6-A0WX-01 TCGA-BH-A1F0-01 TCGA-B6-A0I6-01 TCGA-BH-A18V-01 TCGA-BH-A18K-01 TCGA-BH-A0HL-01 TCGA-BH-A0E0-01 TCGA-A1-A0SB-01 TCGA-A1-A0SB-02 TEST_SAMPLE_1 TEST_SAMPLE_2 TEST_SAMPLE_3 TEST_SAMPLE_4 TEST_SAMPLE_15 TEST_SAMPLE_SOMATIC_HOMOZYGOUS TEST_SAMPLE_SOMATIC_HETEROZYGOUS TEST_SAMPLE_SOMATIC_UNDEFINED diff --git a/test/test_data/study_es_0_import_export/data_clinical_samples.txt b/test/test_data/study_es_0_import_export/data_clinical_samples.txt new file mode 100644 index 00000000000..fd22eb7b077 --- /dev/null +++ b/test/test_data/study_es_0_import_export/data_clinical_samples.txt @@ -0,0 +1,523 @@ +#Patient Identifier Sample Identifier Subtype +#Patient Identifier Sample Identifier Subtype description +#STRING STRING STRING +#1 1 1 +PATIENT_ID SAMPLE_ID SUBTYPE +TCGA-A2-A0EQ TCGA-A2-A0EQ-01 Her2 enriched +TCGA-BH-A18R TCGA-BH-A18R-01 Her2 enriched +TCGA-BH-A0B8 TCGA-BH-A0B8-01 Luminal A +TCGA-BH-A0AW TCGA-BH-A0AW-01 Her2 enriched +TCGA-AO-A03M TCGA-AO-A03M-01 Luminal A +TCGA-A8-A06T TCGA-A8-A06T-01 Luminal A +TCGA-A8-A075 TCGA-A8-A075-01 Her2 enriched +TCGA-E2-A10B TCGA-E2-A10B-01 Luminal A +TCGA-A2-A0CV TCGA-A2-A0CV-01 Luminal A +TCGA-A2-A0EY TCGA-A2-A0EY-01 Luminal B +TCGA-BH-A18J TCGA-BH-A18J-01 Luminal B +TCGA-B6-A0IK TCGA-B6-A0IK-01 Her2 enriched +TCGA-AQ-A04J TCGA-AQ-A04J-01 basal-like +TCGA-E2-A15J TCGA-E2-A15J-01 Luminal A +TCGA-BH-A0DT TCGA-BH-A0DT-01 Luminal A +TCGA-A2-A04V TCGA-A2-A04V-01 Luminal A +TCGA-BH-A1EW TCGA-BH-A1EW-01 Luminal B +TCGA-A8-A09Q TCGA-A8-A09Q-01 Luminal B +TCGA-A2-A0T0 TCGA-A2-A0T0-01 basal-like +TCGA-AO-A124 TCGA-AO-A124-01 basal-like +TCGA-A2-A0YI TCGA-A2-A0YI-01 Luminal A +TCGA-B6-A0IC TCGA-B6-A0IC-01 Luminal B +TCGA-AN-A0XR TCGA-AN-A0XR-01 Luminal B +TCGA-E2-A15R TCGA-E2-A15R-01 Luminal A +TCGA-A2-A04N TCGA-A2-A04N-01 Luminal A +TCGA-A8-A07E TCGA-A8-A07E-01 Luminal A +TCGA-BH-A1EO TCGA-BH-A1EO-01 Luminal A +TCGA-BH-A1F0 TCGA-BH-A1F0-01 basal-like +TCGA-AR-A0U4 TCGA-AR-A0U4-01 basal-like +TCGA-AR-A0TS TCGA-AR-A0TS-01 basal-like +TCGA-B6-A0I2 TCGA-B6-A0I2-01 basal-like +TCGA-BH-A0B0 TCGA-BH-A0B0-01 Luminal A +TCGA-E2-A1B6 TCGA-E2-A1B6-01 Luminal A +TCGA-AO-A0JI TCGA-AO-A0JI-01 Luminal B +TCGA-B6-A0WZ TCGA-B6-A0WZ-01 Luminal A +TCGA-BH-A0C1 TCGA-BH-A0C1-01 Luminal A +TCGA-BH-A0BP TCGA-BH-A0BP-01 Luminal A +TCGA-A2-A0SX TCGA-A2-A0SX-01 basal-like +TCGA-A8-A09I TCGA-A8-A09I-01 Luminal B +TCGA-BH-A0DK TCGA-BH-A0DK-01 Luminal A +TCGA-A8-A086 TCGA-A8-A086-01 Luminal A +TCGA-A8-A07U TCGA-A8-A07U-01 basal-like +TCGA-AO-A12E TCGA-AO-A12E-01 Luminal A +TCGA-A8-A09A TCGA-A8-A09A-01 Luminal A +TCGA-B6-A0RQ TCGA-B6-A0RQ-01 Luminal A +TCGA-A7-A0CJ TCGA-A7-A0CJ-01 Luminal B +TCGA-A8-A099 TCGA-A8-A099-01 Luminal A +TCGA-C8-A12P TCGA-C8-A12P-01 Her2 enriched +TCGA-A8-A08X TCGA-A8-A08X-01 Her2 enriched +TCGA-C8-A131 TCGA-C8-A131-01 basal-like +TCGA-D8-A146 TCGA-D8-A146-01 Luminal A +TCGA-AR-A1AW TCGA-AR-A1AW-01 Luminal A +TCGA-E2-A14Y TCGA-E2-A14Y-01 basal-like +TCGA-B6-A0RI TCGA-B6-A0RI-01 Luminal A +TCGA-AO-A0JA TCGA-AO-A0JA-01 Luminal A +TCGA-C8-A12X TCGA-C8-A12X-01 Luminal B +TCGA-A8-A08P TCGA-A8-A08P-01 Luminal B +TCGA-A8-A091 TCGA-A8-A091-01 Luminal A +TCGA-BH-A0GY TCGA-BH-A0GY-01 Luminal A +TCGA-BH-A0HB TCGA-BH-A0HB-01 Luminal A +TCGA-A8-A08F TCGA-A8-A08F-01 Luminal B +TCGA-E2-A14Q TCGA-E2-A14Q-01 Luminal A +TCGA-E2-A152 TCGA-E2-A152-01 Her2 enriched +TCGA-AO-A0J9 TCGA-AO-A0J9-01 Luminal A +TCGA-AR-A1AO TCGA-AR-A1AO-01 Claudin low +TCGA-A2-A0ER TCGA-A2-A0ER-01 Luminal B +TCGA-E2-A15A TCGA-E2-A15A-01 Luminal B +TCGA-A2-A04W TCGA-A2-A04W-01 Her2 enriched +TCGA-BH-A18S TCGA-BH-A18S-01 Luminal A +TCGA-AO-A03N TCGA-AO-A03N-01 Her2 enriched +TCGA-A8-A06U TCGA-A8-A06U-01 Luminal A +TCGA-A8-A076 TCGA-A8-A076-01 Her2 enriched +TCGA-A2-A0CW TCGA-A2-A0CW-01 Luminal B +TCGA-BH-A0B7 TCGA-BH-A0B7-01 Her2 enriched +TCGA-BH-A0AV TCGA-BH-A0AV-01 basal-like +TCGA-E2-A10C TCGA-E2-A10C-01 Luminal B +TCGA-A8-A0A4 TCGA-A8-A0A4-01 Luminal A +TCGA-BH-A0HK TCGA-BH-A0HK-01 Luminal A +TCGA-E2-A15I TCGA-E2-A15I-01 Luminal A +TCGA-A7-A0DC TCGA-A7-A0DC-01 Luminal A +TCGA-AO-A03V TCGA-AO-A03V-01 Luminal A +TCGA-BH-A1EV TCGA-BH-A1EV-01 Her2 enriched +TCGA-BH-A18K TCGA-BH-A18K-01 basal-like +TCGA-BH-A0E6 TCGA-BH-A0E6-01 basal-like +TCGA-A2-A0D0 TCGA-A2-A0D0-01 basal-like +TCGA-A8-A0AD TCGA-A8-A0AD-01 Luminal A +TCGA-AR-A0TT TCGA-AR-A0TT-01 Luminal B +TCGA-AN-A0FL TCGA-AN-A0FL-01 basal-like +TCGA-A8-A07F TCGA-A8-A07F-01 Luminal A +TCGA-A8-A09X TCGA-A8-A09X-01 Her2 enriched +TCGA-AN-A0FD TCGA-AN-A0FD-01 Luminal A +TCGA-BH-A0C0 TCGA-BH-A0C0-01 Luminal B +TCGA-BH-A0BO TCGA-BH-A0BO-01 Luminal A +TCGA-BH-A0H3 TCGA-BH-A0H3-01 Luminal A +TCGA-AN-A0FT TCGA-AN-A0FT-01 Luminal A +TCGA-BH-A0W3 TCGA-BH-A0W3-01 Luminal B +TCGA-A2-A0SY TCGA-A2-A0SY-01 Luminal A +TCGA-BH-A0BG TCGA-BH-A0BG-01 basal-like +TCGA-B6-A0RP TCGA-B6-A0RP-01 Luminal A +TCGA-AO-A12D TCGA-AO-A12D-01 Her2 enriched +TCGA-AO-A0JJ TCGA-AO-A0JJ-01 Luminal A +TCGA-AN-A0AM TCGA-AN-A0AM-01 Luminal B +TCGA-C8-A132 TCGA-C8-A132-01 Luminal A +TCGA-C8-A12Q TCGA-C8-A12Q-01 Her2 enriched +TCGA-D8-A147 TCGA-D8-A147-01 basal-like +TCGA-BH-A0GZ TCGA-BH-A0GZ-01 Luminal A +TCGA-AR-A1AX TCGA-AR-A1AX-01 Luminal A +TCGA-B6-A0WS TCGA-B6-A0WS-01 Luminal A +TCGA-B6-A0X4 TCGA-B6-A0X4-01 Luminal A +TCGA-B6-A0RH TCGA-B6-A0RH-01 Her2 enriched +TCGA-E2-A159 TCGA-E2-A159-01 basal-like +TCGA-E2-A14X TCGA-E2-A14X-01 basal-like +TCGA-C8-A12Y TCGA-C8-A12Y-01 Luminal A +TCGA-A8-A090 TCGA-A8-A090-01 Luminal A +TCGA-A8-A08O TCGA-A8-A08O-01 Luminal A +TCGA-AO-A0J2 TCGA-AO-A0J2-01 Her2 enriched +TCGA-AR-A1AP TCGA-AR-A1AP-01 Luminal A +TCGA-E2-A14P TCGA-E2-A14P-01 Her2 enriched +TCGA-A1-A0SH TCGA-A1-A0SH-01 Luminal A +TCGA-A8-A08G TCGA-A8-A08G-01 Luminal B +TCGA-BH-A0BW TCGA-BH-A0BW-01 basal-like +TCGA-A2-A04X TCGA-A2-A04X-01 Her2 enriched +TCGA-AO-A03O TCGA-AO-A03O-01 Luminal B +TCGA-BH-A0B2 TCGA-BH-A0B2-01 Luminal A +TCGA-AN-A0XL TCGA-AN-A0XL-01 Luminal A +TCGA-BH-A18T TCGA-BH-A18T-01 Luminal A +TCGA-AR-A1AH TCGA-AR-A1AH-01 basal-like +TCGA-A2-A0EW TCGA-A2-A0EW-01 Luminal A +TCGA-A8-A06R TCGA-A8-A06R-01 Luminal B +TCGA-AQ-A04L TCGA-AQ-A04L-01 Luminal A +TCGA-B6-A0IM TCGA-B6-A0IM-01 Luminal B +TCGA-BH-A0AY TCGA-BH-A0AY-01 Luminal B +TCGA-A2-A04P TCGA-A2-A04P-01 basal-like +TCGA-BH-A0HP TCGA-BH-A0HP-01 Luminal A +TCGA-BH-A0DZ TCGA-BH-A0DZ-01 Her2 enriched +TCGA-E2-A15D TCGA-E2-A15D-01 Luminal A +TCGA-BH-A18L TCGA-BH-A18L-01 Luminal B +TCGA-BH-A0HX TCGA-BH-A0HX-01 Luminal A +TEST_PATIENT_1 TEST_SAMPLE_1 +TCGA-AN-A0XT TCGA-AN-A0XT-01 Luminal A +TCGA-A8-A07C TCGA-A8-A07C-01 basal-like +TCGA-E2-A15L TCGA-E2-A15L-01 Luminal B +TCGA-AN-A03Y TCGA-AN-A03Y-01 Luminal B +TCGA-A2-A0CT TCGA-A2-A0CT-01 Luminal B +TCGA-AR-A0TY TCGA-AR-A0TY-01 Luminal B +TCGA-A8-A09W TCGA-A8-A09W-01 Luminal B +TCGA-AN-A0FK TCGA-AN-A0FK-01 Luminal B +TCGA-A8-A06Z TCGA-A8-A06Z-01 Luminal B +TCGA-E2-A15T TCGA-E2-A15T-01 Luminal B +TCGA-AR-A0TQ TCGA-AR-A0TQ-01 Luminal B +TCGA-AR-A0U2 TCGA-AR-A0U2-01 Luminal B +TCGA-BH-A0DE TCGA-BH-A0DE-01 Luminal A +TCGA-E2-A1B4 TCGA-E2-A1B4-01 Luminal A +TCGA-BH-A0W4 TCGA-BH-A0W4-01 Luminal A +TCGA-BH-A0H0 TCGA-BH-A0H0-01 Luminal B +TCGA-AO-A0JG TCGA-AO-A0JG-01 Luminal A +TCGA-AN-A0FS TCGA-AN-A0FS-01 Luminal A +TCGA-A8-A09G TCGA-A8-A09G-01 Her2 enriched +TCGA-B6-A0WX TCGA-B6-A0WX-01 basal-like +TCGA-BH-A0BJ TCGA-BH-A0BJ-01 Luminal A +TCGA-B6-A0RS TCGA-B6-A0RS-01 Her2 enriched +TCGA-C8-A12N TCGA-C8-A12N-01 Luminal A +TCGA-A2-A0T3 TCGA-A2-A0T3-01 Luminal B +TCGA-AO-A12C TCGA-AO-A12C-01 Luminal A +TCGA-AN-A0AL TCGA-AN-A0AL-01 basal-like +TCGA-A8-A084 TCGA-A8-A084-01 Luminal B +TCGA-A8-A07S TCGA-A8-A07S-01 Luminal B +TCGA-A2-A0CL TCGA-A2-A0CL-01 Her2 enriched +TCGA-A8-A097 TCGA-A8-A097-01 Luminal B +TCGA-E2-A14S TCGA-E2-A14S-01 Luminal B +TCGA-BH-A0BZ TCGA-BH-A0BZ-01 Luminal B +TCGA-E2-A154 TCGA-E2-A154-01 Luminal A +TCGA-C8-A137 TCGA-C8-A137-01 Her2 enriched +TCGA-C8-A12V TCGA-C8-A12V-01 basal-like +TCGA-E2-A1BD TCGA-E2-A1BD-01 Luminal A +TCGA-A1-A0SK TCGA-A1-A0SK-01 basal-like +TCGA-A7-A0CD TCGA-A7-A0CD-01 Luminal A +TCGA-AR-A1AY TCGA-AR-A1AY-01 basal-like +TCGA-BH-A0C3 TCGA-BH-A0C3-01 Luminal B +TCGA-BH-A0BR TCGA-BH-A0BR-01 Luminal A +TCGA-BH-A0RX TCGA-BH-A0RX-01 basal-like +TCGA-A2-A0EO TCGA-A2-A0EO-01 Luminal A +TCGA-AO-A0J7 TCGA-AO-A0J7-01 Luminal B +TCGA-AR-A1AQ TCGA-AR-A1AQ-01 basal-like +TCGA-C8-A1HL TCGA-C8-A1HL-01 Luminal B +TCGA-A2-A04Y TCGA-A2-A04Y-01 Luminal A +TCGA-AO-A03P TCGA-AO-A03P-01 Luminal B +TCGA-A2-A0YT TCGA-A2-A0YT-01 Luminal B +TCGA-A8-A0A2 TCGA-A8-A0A2-01 Luminal A +TCGA-BH-A0HI TCGA-BH-A0HI-01 Luminal A +TCGA-BH-A0B9 TCGA-BH-A0B9-01 basal-like +TCGA-AR-A1AI TCGA-AR-A1AI-01 basal-like +TCGA-E2-A10E TCGA-E2-A10E-01 Luminal A +TCGA-BH-A18U TCGA-BH-A18U-01 Luminal B +TCGA-E2-A14Z TCGA-E2-A14Z-01 Luminal A +TCGA-A2-A0CU TCGA-A2-A0CU-01 Luminal A +TCGA-A2-A04Q TCGA-A2-A04Q-01 basal-like +TCGA-A2-A0EX TCGA-A2-A0EX-01 Luminal A +TCGA-BH-A0HQ TCGA-BH-A0HQ-01 Luminal A +TCGA-B6-A0IN TCGA-B6-A0IN-01 Luminal A +TEST_PATIENT_15 TEST_SAMPLE_15 +TCGA-BH-A18M TCGA-BH-A18M-01 Luminal A +TCGA-E2-A15C TCGA-E2-A15C-01 Luminal A +TCGA-BH-A0BA TCGA-BH-A0BA-01 Luminal A +TCGA-BH-A0HY TCGA-BH-A0HY-01 Her2 enriched +TCGA-BH-A0DS TCGA-BH-A0DS-01 Luminal A +TCGA-AN-A0XS TCGA-AN-A0XS-01 Luminal A +TCGA-A8-A0AB TCGA-A8-A0AB-01 Luminal B +TCGA-A8-A09N TCGA-A8-A09N-01 Luminal B +TCGA-AN-A049 TCGA-AN-A049-01 Luminal B +TCGA-AN-A03X TCGA-AN-A03X-01 Luminal A +TCGA-E2-A15K TCGA-E2-A15K-01 Luminal B +TCGA-AR-A0TZ TCGA-AR-A0TZ-01 Luminal B +TCGA-A2-A0YD TCGA-A2-A0YD-01 Luminal A +TCGA-AN-A041 TCGA-AN-A041-01 Luminal B +TCGA-AN-A0FJ TCGA-AN-A0FJ-01 basal-like +TCGA-A8-A09V TCGA-A8-A09V-01 Luminal A +TCGA-E2-A15S TCGA-E2-A15S-01 Luminal B +TCGA-BH-A0B1 TCGA-BH-A0B1-01 Luminal A +TCGA-B6-A0I5 TCGA-B6-A0I5-01 Luminal A +TCGA-AR-A0U3 TCGA-AR-A0U3-01 Luminal B +TCGA-AR-A0TR TCGA-AR-A0TR-01 Luminal A +TCGA-A2-A0YL TCGA-A2-A0YL-01 Luminal A +TCGA-BH-A0W5 TCGA-BH-A0W5-01 Luminal A +TCGA-A8-A07L TCGA-A8-A07L-01 Luminal B +TCGA-BH-A0DD TCGA-BH-A0DD-01 Luminal B +TCGA-AN-A0AS TCGA-AN-A0AS-01 Luminal B +TCGA-BH-A0BQ TCGA-BH-A0BQ-01 Luminal A +TCGA-B6-A0WY TCGA-B6-A0WY-01 Luminal A +TCGA-E2-A1B5 TCGA-E2-A1B5-01 basal-like +TCGA-A2-A0YC TCGA-A2-A0YC-01 Luminal A +TCGA-A8-A085 TCGA-A8-A085-01 Luminal B +TCGA-BH-A0DL TCGA-BH-A0DL-01 basal-like +TCGA-AN-A0AK TCGA-AN-A0AK-01 Luminal B +TCGA-AN-A0FZ TCGA-AN-A0FZ-01 Luminal A +TCGA-A2-A0T4 TCGA-A2-A0T4-01 Luminal B +TCGA-C8-A12O TCGA-C8-A12O-01 Luminal A +TCGA-C8-A130 TCGA-C8-A130-01 Her2 enriched +TCGA-AN-A04A TCGA-AN-A04A-01 Luminal A +TCGA-A2-A0CM TCGA-A2-A0CM-01 basal-like +TCGA-AO-A12B TCGA-AO-A12B-01 Luminal B +TCGA-A8-A096 TCGA-A8-A096-01 Luminal B +TCGA-E2-A153 TCGA-E2-A153-01 Luminal A +TCGA-D8-A145 TCGA-D8-A145-01 Luminal A +TCGA-E2-A14R TCGA-E2-A14R-01 basal-like +TCGA-C8-A12W TCGA-C8-A12W-01 Luminal B +TCGA-C8-A138 TCGA-C8-A138-01 Her2 enriched +TCGA-A8-A0A1 TCGA-A8-A0A1-01 Luminal A +TCGA-BH-A0H9 TCGA-BH-A0H9-01 Luminal A +TCGA-BH-A0EE TCGA-BH-A0EE-01 Her2 enriched +TCGA-A1-A0SJ TCGA-A1-A0SJ-01 Luminal A +TCGA-AO-A0J8 TCGA-AO-A0J8-01 Luminal A +TCGA-A1-A0SB TCGA-A1-A0SB-01 +TCGA-A1-A0SB TCGA-A1-A0SB-02 +TCGA-C8-A1HM TCGA-C8-A1HM-01 Luminal B +TCGA-AR-A1AR TCGA-AR-A1AR-01 basal-like +TCGA-BH-A0HA TCGA-BH-A0HA-01 Luminal A +TCGA-BH-A0B4 TCGA-BH-A0B4-01 Luminal A +TCGA-A2-A0CZ TCGA-A2-A0CZ-01 Luminal A +TCGA-A8-A0A9 TCGA-A8-A0A9-01 Luminal B +TCGA-A2-A0EU TCGA-A2-A0EU-01 Luminal A +TCGA-B6-A0IO TCGA-B6-A0IO-01 Luminal A +TCGA-AR-A1AJ TCGA-AR-A1AJ-01 basal-like +TCGA-A8-A06P TCGA-A8-A06P-01 Luminal A +TCGA-BH-A0EA TCGA-BH-A0EA-01 Luminal A +TCGA-AN-A0XN TCGA-AN-A0XN-01 Luminal A +TCGA-BH-A18V TCGA-BH-A18V-01 basal-like +TCGA-BH-A0E9 TCGA-BH-A0E9-01 Luminal A +TCGA-BH-A0DX TCGA-BH-A0DX-01 Luminal A +TCGA-A2-A04R TCGA-A2-A04R-01 Luminal B +TCGA-E2-A15F TCGA-E2-A15F-01 Luminal A +TCGA-E2-A106 TCGA-E2-A106-01 Luminal A +TCGA-BH-A18N TCGA-BH-A18N-01 Luminal A +TCGA-B6-A0IG TCGA-B6-A0IG-01 Luminal A +TCGA-AN-A0XV TCGA-AN-A0XV-01 Luminal A +TCGA-BH-A1ES TCGA-BH-A1ES-01 Luminal A +TCGA-BH-A0E1 TCGA-BH-A0E1-01 Luminal A +TCGA-BH-A0DP TCGA-BH-A0DP-01 Luminal A +TCGA-BH-A18F TCGA-BH-A18F-01 Luminal B +TCGA-AR-A0TW TCGA-AR-A0TW-01 Luminal A +TCGA-A2-A0D3 TCGA-A2-A0D3-01 Luminal A +TCGA-E2-A10F TCGA-E2-A10F-01 Luminal A +TCGA-A8-A079 TCGA-A8-A079-01 Luminal B +TCGA-A8-A06X TCGA-A8-A06X-01 Luminal B +TCGA-A8-A09M TCGA-A8-A09M-01 Luminal B +TCGA-B6-A0I6 TCGA-B6-A0I6-01 +TCGA-A2-A0YM TCGA-A2-A0YM-01 basal-like +TCGA-A8-A09E TCGA-A8-A09E-01 Luminal B +TCGA-AN-A04D TCGA-AN-A04D-01 basal-like +TCGA-BH-A0DG TCGA-BH-A0DG-01 Luminal A +TCGA-AN-A0AR TCGA-AN-A0AR-01 basal-like +TCGA-AO-A0JE TCGA-AO-A0JE-01 Her2 enriched +TCGA-BH-A0BL TCGA-BH-A0BL-01 basal-like +TCGA-B6-A0WV TCGA-B6-A0WV-01 Luminal B +TCGA-B6-A0X7 TCGA-B6-A0X7-01 Luminal A +TEST_PATIENT_NAMESPACE TEST_SAMPLE_SOMATIC_HETEROZYGOUS +TCGA-A1-A0SM TCGA-A1-A0SM-01 Luminal B +TCGA-A8-A07I TCGA-A8-A07I-01 Her2 enriched +TCGA-BH-A0H6 TCGA-BH-A0H6-01 Luminal A +TCGA-C8-A12L TCGA-C8-A12L-01 Her2 enriched +TCGA-AO-A129 TCGA-AO-A129-01 basal-like +TCGA-AN-A0FY TCGA-AN-A0FY-01 Luminal B +TCGA-AN-A0AJ TCGA-AN-A0AJ-01 Luminal B +TCGA-A2-A0T5 TCGA-A2-A0T5-01 Luminal A +TCGA-A2-A0ST TCGA-A2-A0ST-01 basal-like +TCGA-A8-A082 TCGA-A8-A082-01 Luminal B +TCGA-AO-A0JM TCGA-AO-A0JM-01 Luminal B +TCGA-B6-A0RU TCGA-B6-A0RU-01 basal-like +TCGA-AO-A12A TCGA-AO-A12A-01 Luminal A +TCGA-C8-A1HN TCGA-C8-A1HN-01 Luminal B +TCGA-B6-A0RM TCGA-B6-A0RM-01 Luminal A +TCGA-AR-A1AS TCGA-AR-A1AS-01 Luminal A +TCGA-E2-A156 TCGA-E2-A156-01 Luminal A +TCGA-BH-A0BD TCGA-BH-A0BD-01 Luminal B +TCGA-E2-A105 TCGA-E2-A105-01 Luminal A +TCGA-A8-A095 TCGA-A8-A095-01 Luminal B +TCGA-A8-A08T TCGA-A8-A08T-01 Luminal A +TCGA-C8-A135 TCGA-C8-A135-01 Her2 enriched +TCGA-C8-A12T TCGA-C8-A12T-01 Her2 enriched +TCGA-D8-A142 TCGA-D8-A142-01 basal-like +TCGA-A8-A08B TCGA-A8-A08B-01 Her2 enriched +TCGA-AO-A0J5 TCGA-AO-A0J5-01 Luminal A +TCGA-AR-A1AK TCGA-AR-A1AK-01 Luminal A +TCGA-C8-A1HF TCGA-C8-A1HF-01 Her2 enriched +TCGA-B6-A0RE TCGA-B6-A0RE-01 basal-like +TCGA-BH-A0HF TCGA-BH-A0HF-01 Luminal A +TCGA-A8-A08L TCGA-A8-A08L-01 Her2 enriched +TCGA-D8-A13Y TCGA-D8-A13Y-01 Luminal B +TCGA-BH-A0BT TCGA-BH-A0BT-01 Luminal A +TCGA-A2-A0EM TCGA-A2-A0EM-01 Luminal A +TCGA-A1-A0SE TCGA-A1-A0SE-01 Luminal A +TEST_PATIENT_4 TEST_SAMPLE_4 +TCGA-BH-A0HO TCGA-BH-A0HO-01 Luminal A +TCGA-B6-A0IP TCGA-B6-A0IP-01 Luminal A +TCGA-BH-A0B3 TCGA-BH-A0B3-01 basal-like +TCGA-A8-A06Q TCGA-A8-A06Q-01 Luminal B +TCGA-BH-A0EB TCGA-BH-A0EB-01 Luminal A +TCGA-A2-A0EV TCGA-A2-A0EV-01 Luminal A +TCGA-BH-A0AZ TCGA-BH-A0AZ-01 Luminal A +TCGA-B6-A0IH TCGA-B6-A0IH-01 Luminal A +TCGA-E2-A15E TCGA-E2-A15E-01 Luminal A +TCGA-E2-A107 TCGA-E2-A107-01 Luminal B +TCGA-BH-A0HW TCGA-BH-A0HW-01 Luminal B +TCGA-AN-A0XU TCGA-AN-A0XU-01 basal-like +TCGA-A8-A07B TCGA-A8-A07B-01 Her2 enriched +TCGA-BH-A0E2 TCGA-BH-A0E2-01 Luminal A +TCGA-BH-A0DQ TCGA-BH-A0DQ-01 Luminal A +TCGA-AR-A0TX TCGA-AR-A0TX-01 Her2 enriched +TCGA-A2-A0D4 TCGA-A2-A0D4-01 Luminal B +TCGA-A2-A0CS TCGA-A2-A0CS-01 Luminal A +TCGA-E2-A15M TCGA-E2-A15M-01 Luminal B +TCGA-A8-A06Y TCGA-A8-A06Y-01 Luminal A +TCGA-A7-A13F TCGA-A7-A13F-01 Luminal B +TCGA-A2-A0YF TCGA-A2-A0YF-01 Luminal A +TCGA-A8-A09T TCGA-A8-A09T-01 Luminal A +TCGA-BH-A0W7 TCGA-BH-A0W7-01 Luminal A +TCGA-AR-A0U1 TCGA-AR-A0U1-01 basal-like +TCGA-AR-A0TP TCGA-AR-A0TP-01 basal-like +TCGA-B6-A0I8 TCGA-B6-A0I8-01 Luminal A +TCGA-A8-A09D TCGA-A8-A09D-01 Luminal B +TCGA-AN-A04C TCGA-AN-A04C-01 Her2 enriched +TEST_PATIENT_2 TEST_SAMPLE_2 +TCGA-AO-A0JF TCGA-AO-A0JF-01 Luminal A +TCGA-B6-A0WW TCGA-B6-A0WW-01 Luminal B +TCGA-A8-A07J TCGA-A8-A07J-01 Luminal A +TCGA-BH-A0H7 TCGA-BH-A0H7-01 Luminal A +TCGA-A2-A0SU TCGA-A2-A0SU-01 Luminal A +TCGA-A2-A0T6 TCGA-A2-A0T6-01 Luminal A +TCGA-C8-A12M TCGA-C8-A12M-01 Luminal B +TCGA-AO-A12H TCGA-AO-A12H-01 Luminal A +TCGA-AN-A0FX TCGA-AN-A0FX-01 basal-like +TCGA-B6-A0RT TCGA-B6-A0RT-01 basal-like +TCGA-A8-A083 TCGA-A8-A083-01 Luminal A +TCGA-A8-A07R TCGA-A8-A07R-01 basal-like +TCGA-E2-A155 TCGA-E2-A155-01 Luminal B +TCGA-E2-A1BC TCGA-E2-A1BC-01 Luminal A +TCGA-E2-A14T TCGA-E2-A14T-01 Luminal A +TCGA-AR-A1AT TCGA-AR-A1AT-01 Her2 enriched +TCGA-A8-A07Z TCGA-A8-A07Z-01 Luminal B +TCGA-B6-A0RL TCGA-B6-A0RL-01 Luminal B +TCGA-BH-A0BC TCGA-BH-A0BC-01 Luminal A +TEST_PATIENT_3 TEST_SAMPLE_3 +TCGA-B6-A0X0 TCGA-B6-A0X0-01 Luminal A +TCGA-A8-A08S TCGA-A8-A08S-01 Luminal B +TCGA-C8-A12U TCGA-C8-A12U-01 Luminal B +TCGA-A8-A094 TCGA-A8-A094-01 Her2 enriched +TCGA-A7-A0CE TCGA-A7-A0CE-01 basal-like +TCGA-C8-A1HG TCGA-C8-A1HG-01 Luminal B +TCGA-AR-A1AL TCGA-AR-A1AL-01 Luminal A +TCGA-A8-A08C TCGA-A8-A08C-01 Luminal A +TCGA-BH-A0BS TCGA-BH-A0BS-01 Luminal A +TCGA-A2-A0EN TCGA-A2-A0EN-01 Luminal A +TCGA-AO-A0J6 TCGA-AO-A0J6-01 basal-like +TCGA-A1-A0SD TCGA-A1-A0SD-01 Luminal A +TCGA-D8-A13Z TCGA-D8-A13Z-01 Her2 enriched +TCGA-A8-A08I TCGA-A8-A08I-01 Luminal B +TCGA-BH-A18P TCGA-BH-A18P-01 Her2 enriched +TCGA-BH-A0HL TCGA-BH-A0HL-01 +TCGA-A8-A0A7 TCGA-A8-A0A7-01 Her2 enriched +TCGA-B6-A0IQ TCGA-B6-A0IQ-01 basal-like +TCGA-A2-A0ES TCGA-A2-A0ES-01 Luminal A +TCGA-A2-A0CX TCGA-A2-A0CX-01 Her2 enriched +TCGA-BH-A0AU TCGA-BH-A0AU-01 Luminal B +TCGA-E2-A15H TCGA-E2-A15H-01 Luminal A +TCGA-A8-A06N TCGA-A8-A06N-01 Luminal B +TCGA-BH-A18H TCGA-BH-A18H-01 Luminal A +TCGA-A7-A0DB TCGA-A7-A0DB-01 Luminal A +TCGA-AQ-A04H TCGA-AQ-A04H-01 Luminal B +TCGA-BH-A1EU TCGA-BH-A1EU-01 Luminal A +TCGA-E2-A108 TCGA-E2-A108-01 Claudin low +TCGA-BH-A0E7 TCGA-BH-A0E7-01 Luminal A +TCGA-AN-A046 TCGA-AN-A046-01 Luminal A +TCGA-A2-A0CP TCGA-A2-A0CP-01 Luminal A +TCGA-A2-A0D1 TCGA-A2-A0D1-01 Her2 enriched +TCGA-A2-A0YG TCGA-A2-A0YG-01 Luminal B +TCGA-AO-A126 TCGA-AO-A126-01 Luminal A +TCGA-B6-A0IA TCGA-B6-A0IA-01 Luminal A +TCGA-E2-A15P TCGA-E2-A15P-01 Luminal A +TCGA-AN-A0XP TCGA-AN-A0XP-01 Luminal A +TCGA-A8-A07G TCGA-A8-A07G-01 Luminal A +TCGA-A8-A09K TCGA-A8-A09K-01 Luminal B +TCGA-A8-A07O TCGA-A8-A07O-01 basal-like +TCGA-A8-A09C TCGA-A8-A09C-01 Luminal B +TCGA-B6-A0I9 TCGA-B6-A0I9-01 Her2 enriched +TCGA-BH-A0DI TCGA-BH-A0DI-01 Luminal A +TCGA-AO-A0JC TCGA-AO-A0JC-01 Luminal B +TCGA-A2-A0SV TCGA-A2-A0SV-01 Luminal B +TCGA-A2-A0T7 TCGA-A2-A0T7-01 Luminal A +TCGA-A1-A0SO TCGA-A1-A0SO-01 basal-like +TCGA-E2-A1B0 TCGA-E2-A1B0-01 Her2 enriched +TCGA-D8-A140 TCGA-D8-A140-01 Luminal B +TCGA-BH-A0BF TCGA-BH-A0BF-01 Luminal B +TCGA-AO-A12G TCGA-AO-A12G-01 Luminal A +TCGA-A8-A07W TCGA-A8-A07W-01 Luminal B +TCGA-A8-A08Z TCGA-A8-A08Z-01 Luminal A +TCGA-AN-A0FW TCGA-AN-A0FW-01 Luminal A +TCGA-C8-A133 TCGA-C8-A133-01 Luminal A +TCGA-AR-A1AU TCGA-AR-A1AU-01 Luminal A +TCGA-B6-A0RO TCGA-B6-A0RO-01 Luminal A +TCGA-E2-A14W TCGA-E2-A14W-01 Luminal B +TCGA-E2-A158 TCGA-E2-A158-01 basal-like +TCGA-B6-A0X5 TCGA-B6-A0X5-01 Luminal B +TCGA-A8-A093 TCGA-A8-A093-01 Luminal A +TCGA-B6-A0WT TCGA-B6-A0WT-01 Luminal A +TCGA-A8-A08R TCGA-A8-A08R-01 basal-like +TCGA-BH-A0C7 TCGA-BH-A0C7-01 Luminal B +TCGA-BH-A0BV TCGA-BH-A0BV-01 Luminal A +TCGA-B6-A0RG TCGA-B6-A0RG-01 Luminal A +TCGA-AO-A0J3 TCGA-AO-A0J3-01 Luminal B +TCGA-C8-A12Z TCGA-C8-A12Z-01 Her2 enriched +TCGA-A7-A0CH TCGA-A7-A0CH-01 Luminal A +TCGA-A8-A08J TCGA-A8-A08J-01 Her2 enriched +TCGA-E2-A14O TCGA-E2-A14O-01 Luminal B +TCGA-E2-A150 TCGA-E2-A150-01 basal-like +TCGA-A8-A08H TCGA-A8-A08H-01 basal-like +TCGA-BH-A0B5 TCGA-BH-A0B5-01 Luminal B +TCGA-E2-A10A TCGA-E2-A10A-01 Luminal B +TCGA-A7-A0D9 TCGA-A7-A0D9-01 Luminal A +TCGA-A8-A0A6 TCGA-A8-A0A6-01 Luminal A +TCGA-BH-A18Q TCGA-BH-A18Q-01 basal-like +TCGA-A8-A06O TCGA-A8-A06O-01 Luminal B +TCGA-A2-A0ET TCGA-A2-A0ET-01 Luminal A +TCGA-A2-A0CY TCGA-A2-A0CY-01 Her2 enriched +TCGA-A8-A09Z TCGA-A8-A09Z-01 Luminal B +TCGA-BH-A18I TCGA-BH-A18I-01 Luminal A +TCGA-E2-A15G TCGA-E2-A15G-01 Luminal A +TCGA-AO-A03L TCGA-AO-A03L-01 Her2 enriched +TCGA-BH-A0HU TCGA-BH-A0HU-01 Luminal B +TCGA-BH-A1ET TCGA-BH-A1ET-01 Luminal A +TCGA-B6-A0IJ TCGA-B6-A0IJ-01 basal-like +TCGA-A7-A0DA TCGA-A7-A0DA-01 basal-like +TCGA-E2-A109 TCGA-E2-A109-01 Luminal B +TCGA-E2-A15O TCGA-E2-A15O-01 Luminal A +TCGA-AN-A0FF TCGA-AN-A0FF-01 Luminal B +TCGA-A2-A0T1 TCGA-A2-A0T1-01 Her2 enriched +TCGA-A2-A0YH TCGA-A2-A0YH-01 Luminal B +TCGA-A2-A0CQ TCGA-A2-A0CQ-01 Luminal A +TCGA-A2-A0D2 TCGA-A2-A0D2-01 basal-like +TEST_PATIENT_NAMESPACE TEST_SAMPLE_SOMATIC_UNDEFINED +TCGA-BH-A0DO TCGA-BH-A0DO-01 Luminal A +TCGA-BH-A0E0 TCGA-BH-A0E0-01 basal-like +TCGA-B6-A0IB TCGA-B6-A0IB-01 Luminal B +TCGA-AO-A125 TCGA-AO-A125-01 Luminal A +TCGA-BH-A0WA TCGA-BH-A0WA-01 basal-like +TCGA-AN-A0XO TCGA-AN-A0XO-01 Luminal A +TCGA-AR-A0TV TCGA-AR-A0TV-01 Luminal B +TCGA-AN-A0XW TCGA-AN-A0XW-01 Luminal B +TCGA-A7-A13D TCGA-A7-A13D-01 basal-like +TCGA-A8-A09R TCGA-A8-A09R-01 Luminal B +TEST_PATIENT_NAMESPACE TEST_SAMPLE_SOMATIC_HOMOZYGOUS +TCGA-A8-A09B TCGA-A8-A09B-01 Luminal A +TCGA-BH-A0H5 TCGA-BH-A0H5-01 Luminal A +TCGA-AO-A0JD TCGA-AO-A0JD-01 Luminal B +TCGA-BH-A0BM TCGA-BH-A0BM-01 Luminal A +TCGA-BH-A0DH TCGA-BH-A0DH-01 Luminal A +TCGA-E2-A1B1 TCGA-E2-A1B1-01 Luminal A +TCGA-A2-A0SW TCGA-A2-A0SW-01 Luminal B +TCGA-AN-A0FN TCGA-AN-A0FN-01 Luminal A +TCGA-AO-A12F TCGA-AO-A12F-01 basal-like +TCGA-AN-A0FV TCGA-AN-A0FV-01 Her2 enriched +TCGA-A8-A07P TCGA-A8-A07P-01 Luminal A +TCGA-A8-A081 TCGA-A8-A081-01 Her2 enriched +TCGA-B6-A0RV TCGA-B6-A0RV-01 Luminal A +TCGA-C8-A12K TCGA-C8-A12K-01 basal-like +TCGA-AO-A0JL TCGA-AO-A0JL-01 basal-like +TCGA-C8-A134 TCGA-C8-A134-01 basal-like +TCGA-AR-A1AV TCGA-AR-A1AV-01 Luminal B +TCGA-B6-A0RN TCGA-B6-A0RN-01 Luminal A +TCGA-E2-A14V TCGA-E2-A14V-01 Her2 enriched +TCGA-A8-A092 TCGA-A8-A092-01 Her2 enriched +TCGA-D8-A141 TCGA-D8-A141-01 Luminal A +TCGA-C8-A1HI TCGA-C8-A1HI-01 Luminal A +TCGA-AR-A1AN TCGA-AR-A1AN-01 Luminal A +TCGA-AO-A0J4 TCGA-AO-A0J4-01 basal-like +TCGA-A8-A08A TCGA-A8-A08A-01 Luminal A +TCGA-A7-A0CG TCGA-A7-A0CG-01 Luminal A +TCGA-BH-A0EI TCGA-BH-A0EI-01 Luminal A +TCGA-E2-A14N TCGA-E2-A14N-01 basal-like diff --git a/test/test_data/study_es_0_import_export/data_mutations.txt b/test/test_data/study_es_0_import_export/data_mutations.txt new file mode 100644 index 00000000000..5d181f48041 --- /dev/null +++ b/test/test_data/study_es_0_import_export/data_mutations.txt @@ -0,0 +1,35 @@ +Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer HGVSp_Short t_alt_count t_ref_count n_alt_count n_ref_count +BRCA1 672 genome.wustl.edu GRCh37 17 41243581 41243581 + Missense_Mutation SNP G A A rs80357262 NA TEST_SAMPLE_SOMATIC_UNDEFINED TCGA-A1-A0SB-10 A G NA NA NA NA Unknown NA Somatic Phase_IV Capture NA 1 dbGAP IlluminaGAIIx +BRCA1 672 genome.wustl.edu GRCh37 17 41243581 41243581 + Missense_Mutation SNP G A A rs80357262 NA TEST_SAMPLE_SOMATIC_HETEROZYGOUS TCGA-A1-A0SB-10 A G NA NA NA NA Unknown NA Somatic Phase_IV Capture NA 1 dbGAP IlluminaGAIIx +BRCA1 672 genome.wustl.edu GRCh37 17 41243581 41243581 + Missense_Mutation SNP G A A rs80357262 NA TEST_SAMPLE_SOMATIC_HOMOZYGOUS TCGA-A1-A0SB-10 A G NA NA NA NA Unknown NA Somatic Phase_IV Capture NA 1 dbGAP IlluminaGAIIx +ACP3 55 genome.wustl.edu GRCh37 3 132047117 132047117 + Missense_Mutation SNP C T T NA NA TEST_SAMPLE_15 NA NA NA NA NA NA NA NA NA Somatic NA NA NA NA NA NA +ACP3 55 genome.wustl.edu GRCh37 3 132047117 132047117 + Missense_Mutation SNP C T T NA NA TEST_SAMPLE_4 NA NA NA NA NA NA NA NA NA Somatic NA NA NA NA NA NA +ACP3 55 genome.wustl.edu GRCh37 3 132047117 132047117 + Missense_Mutation SNP C T T NA NA TEST_SAMPLE_3 NA NA NA NA NA NA NA NA NA Somatic NA NA NA NA NA NA +ACP3 55 genome.wustl.edu GRCh37 3 132047117 132047117 + Missense_Mutation SNP C T T NA NA TEST_SAMPLE_2 NA NA NA NA NA NA NA NA NA Somatic NA NA NA NA NA NA +ACP3 55 genome.wustl.edu GRCh37 3 132047117 132047117 + Missense_Mutation SNP C T T NA NA TEST_SAMPLE_1 NA NA NA NA NA NA NA NA NA Somatic NA NA NA NA NA NA +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 +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 +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 +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 +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 +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 +TMEM247 388946 genome.wustl.edu GRCh37 2 46707888 46707888 + Frame_Shift_Del DEL G - - NA NA TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 G G NA NA NA NA Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx +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 +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 +DTNB 1838 genome.wustl.edu GRCh37 2 25678299 25678299 + Missense_Mutation SNP C T T NA NA TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 C C NA NA NA NA Unknown Untested Somatic Phase_IV WXS none 1 dbGAP Illumina GAIIx +BRCA1 672 genome.wustl.edu GRCh37 17 41243581 41243581 + Nonsense_Mutation SNP G A A rs80357262 NA TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 A G NA NA NA NA Unknown NA Germline Phase_IV Capture NA 1 dbGAP IlluminaGAIIx +BRCA1 672 genome.wustl.edu GRCh37 17 41201181 41201181 + Missense_Mutation SNP C A A rs80357069 byCluster TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 C C NA NA NA NA Unknown NA Somatic Phase_IV Capture NA 1 dbGAP Illumina GAIIx +ATM 472 genome.wustl.edu GRCh37 11 108173702 108173702 + Frame_Shift_Del DEL G - - NA NA TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 - G NA NA NA NA Unknown NA Germline Phase_IV Capture NA 1 dbGAP IlluminaGAIIx +ATM 472 genome.wustl.edu GRCh37 11 108106472 108106472 + Frame_Shift_Del DEL T - - novel unknown TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 T T NA NA NA NA Unknown NA Somatic Phase_IV Capture NA 1 dbGAP Illumina GAIIx +BRCA2 675 genome.wustl.edu GRCh37 13 108106473 108106473 + Nonsense_Mutation SNP T C C NA NA TCGA-A1-A0SB-01 TCGA-A1-A0SB-10 NA NA NA NA NA NA NA NA Germline NA NA NA NA NA NA +BRCA2 675 genome.wustl.edu GRCh37 13 108106484 108106484 + Missense_Mutation SNP T C C NA NA TCGA-BH-A0E0-01 TCGA-BH-A0E0-10 NA NA NA NA NA NA NA NA Somatic NA NA NA NA NA NA +BRCA2 675 genome.wustl.edu GRCh37 13 108106483 108106483 + Missense_Mutation SNP T C C NA NA TCGA-BH-A0HL-01 TCGA-BH-A0HL-10 NA NA NA NA NA NA NA NA Germline NA NA NA NA NA NA +BRCA2 675 genome.wustl.edu GRCh37 13 108106482 108106482 + In_Frame_Del DEL T - - NA NA TCGA-BH-A18K-01 TCGA-BH-A18K-10 NA NA NA NA NA NA NA NA Somatic NA NA NA NA NA NA +BRCA2 675 genome.wustl.edu GRCh37 13 108106481 108106481 + In_Frame_Del DEL T - - NA NA TCGA-BH-A18V-01 TCGA-BH-A18V-10 NA NA NA NA NA NA NA NA Germline NA NA NA NA NA NA +BRCA2 675 genome.wustl.edu GRCh37 13 108106480 108106480 + Nonsense_Mutation SNP T C C NA NA TCGA-B6-A0I6-01 TCGA-B6-A0I6-10 NA NA NA NA NA NA NA NA Somatic NA NA NA NA NA NA +BRCA2 675 genome.wustl.edu GRCh37 13 108106479 108106479 + Nonsense_Mutation SNP T C C NA NA TCGA-BH-A1F0-01 TCGA-BH-A1F0-10 NA NA NA NA NA NA NA NA Germline NA NA NA NA NA NA +BRCA2 675 genome.wustl.edu GRCh37 13 108106478 108106478 + Missense_Mutation SNP T C C NA NA TCGA-B6-A0WX-01 TCGA-B6-A0WX-10 NA NA NA NA NA NA NA NA Somatic NA NA NA NA NA NA +BRCA2 675 genome.wustl.edu GRCh37 13 108106477 108106477 + Missense_Mutation SNP T C C NA NA TCGA-AR-A1AR-01 TCGA-AR-A1AR-10 NA NA NA NA NA NA NA NA Germline NA NA NA NA NA NA +BRCA2 675 genome.wustl.edu GRCh37 13 108106476 108106476 + In_Frame_Del DEL T - - NA NA TCGA-A2-A0CM-01 TCGA-A2-A0CM-10 NA NA NA NA NA NA NA NA Somatic NA NA NA NA NA NA +BRCA2 675 genome.wustl.edu GRCh37 13 108106475 108106475 + In_Frame_Del DEL T - - NA NA TCGA-A1-A0SK-01 TCGA-A1-A0SK-10 NA NA NA NA NA NA NA NA Germline NA NA NA NA NA NA +BRCA2 675 genome.wustl.edu GRCh37 13 108106474 108106474 + Nonsense_Mutation SNP T C C NA NA TCGA-A2-A04P-01 TCGA-A2-A04P-10 NA NA NA NA NA NA NA NA Somatic NA NA NA NA NA NA diff --git a/test/test_data/study_es_0_import_export/meta_clinical_samples.txt b/test/test_data/study_es_0_import_export/meta_clinical_samples.txt new file mode 100644 index 00000000000..c3cdc6773ed --- /dev/null +++ b/test/test_data/study_es_0_import_export/meta_clinical_samples.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: study_es_0_import_export +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_samples.txt diff --git a/test/test_data/study_es_0_import_export/meta_mutations.txt b/test/test_data/study_es_0_import_export/meta_mutations.txt new file mode 100644 index 00000000000..c9bb93bfae1 --- /dev/null +++ b/test/test_data/study_es_0_import_export/meta_mutations.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: study_es_0_import_export +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +data_filename: data_mutations.txt +stable_id: mutations +show_profile_in_analysis_tab: true +profile_name: Mutations +profile_description: Mutation data from whole exome sequencing. diff --git a/test/test_data/study_es_0_import_export/meta_study.txt b/test/test_data/study_es_0_import_export/meta_study.txt new file mode 100644 index 00000000000..277e2cff81f --- /dev/null +++ b/test/test_data/study_es_0_import_export/meta_study.txt @@ -0,0 +1,9 @@ +type_of_cancer: brca +cancer_study_identifier: study_es_0_import_export +name: Test study es_0 +description: Test study es_0 +citation: Cell 2018 +pmid: 29625048,29596782,29622463,29617662,29625055,29625050 +groups: SU2C-PI3K;PUBLIC;GDAC +add_global_case_list: true +reference_genome: hg19