Merge pull request #96 from thehyve/ngs-test-data-fixes

NGS test data fixes to enable display of derived variables
thehyve · Dec 16, 2019 · aca3c9b · aca3c9b
2 parents 031832f + c37e995
commit aca3c9b
Show file tree

Hide file tree

Showing 26 changed files with 14 additions and 1 deletion.
diff --git a/test_data/test_data_NGS/config/ontology_config.json b/test_data/test_data_NGS/config/ontology_config.json
@@ -118,6 +118,14 @@
         {
           "name": "03. Biomaterial type",
           "concept_code": "Biomaterial.type"
+        },
+        {
+          "name": "04. Library strategy",
+          "concept_code": "Biomaterial.library_strategy"
+        },
+        {
+          "name": "05. Analysis type",
+          "concept_code": "Biomaterial.analysis_type"
         }
       ]
     },

diff --git a/test_data/test_data_NGS/config/sources_config.json b/test_data/test_data_NGS/config/sources_config.json
@@ -382,7 +382,8 @@
   "codebooks": {
     "studies/individual.txt": "studies/individual_codebook.txt",
     "studies/diagnosis.txt": "studies/diagnosis_codebook.txt",
-    "studies/death.txt": "studies/death_codebook.txt"
+    "studies/death.txt": "studies/death_codebook.txt",
+    "clinic/RDP-Patient.tab": "clinic/RDP-Patient_codebook.txt"
   },
   "file_format": {
     "studies/individual.txt": {

diff --git a/...dropzone/alternative/NGS/pmc_test1.maf.gz → ...zone/alternative/NGS/pmc_test1_WGS.maf.gz b/...dropzone/alternative/NGS/pmc_test1.maf.gz → ...zone/alternative/NGS/pmc_test1_WGS.maf.gz
diff --git a/...one/alternative/NGS/pmc_test1.maf.gz.sha1 → ...alternative/NGS/pmc_test1_WGS.maf.gz.sha1 b/...one/alternative/NGS/pmc_test1.maf.gz.sha1 → ...alternative/NGS/pmc_test1_WGS.maf.gz.sha1
diff --git a/...dropzone/alternative/NGS/pmc_test2.maf.gz → ...zone/alternative/NGS/pmc_test2_WGS.maf.gz b/...dropzone/alternative/NGS/pmc_test2.maf.gz → ...zone/alternative/NGS/pmc_test2_WGS.maf.gz
diff --git a/...one/alternative/NGS/pmc_test2.maf.gz.sha1 → ...alternative/NGS/pmc_test2_WGS.maf.gz.sha1 b/...one/alternative/NGS/pmc_test2.maf.gz.sha1 → ...alternative/NGS/pmc_test2_WGS.maf.gz.sha1
diff --git a/...NGS/dropzone/alternative/NGS/pmc_test.seg → ...dropzone/alternative/NGS/pmc_test_WXS.seg b/...NGS/dropzone/alternative/NGS/pmc_test.seg → ...dropzone/alternative/NGS/pmc_test_WXS.seg
diff --git a/...ropzone/alternative/NGS/pmc_test.seg.sha1 → ...one/alternative/NGS/pmc_test_WXS.seg.sha1 b/...ropzone/alternative/NGS/pmc_test.seg.sha1 → ...one/alternative/NGS/pmc_test_WXS.seg.sha1
diff --git a/...native/NGS/pmc_test_all_data_by_genes.txt → ...ve/NGS/pmc_test_WXS_all_data_by_genes.txt b/...native/NGS/pmc_test_all_data_by_genes.txt → ...ve/NGS/pmc_test_WXS_all_data_by_genes.txt
diff --git a/...e/NGS/pmc_test_all_data_by_genes.txt.sha1 → ...S/pmc_test_WXS_all_data_by_genes.txt.sha1 b/...e/NGS/pmc_test_all_data_by_genes.txt.sha1 → ...S/pmc_test_WXS_all_data_by_genes.txt.sha1
diff --git a/...NGS/pmc_test_all_thresholded.by_genes.txt → ...pmc_test_WXS_all_thresholded.by_genes.txt b/...NGS/pmc_test_all_thresholded.by_genes.txt → ...pmc_test_WXS_all_thresholded.by_genes.txt
diff --git a/...mc_test_all_thresholded.by_genes.txt.sha1 → ...est_WXS_all_thresholded.by_genes.txt.sha1 b/...mc_test_all_thresholded.by_genes.txt.sha1 → ...est_WXS_all_thresholded.by_genes.txt.sha1
diff --git a/test_data/test_data_NGS/dropzone/alternative/clinic/RDP-Patient_codebook.txt b/test_data/test_data_NGS/dropzone/alternative/clinic/RDP-Patient_codebook.txt
@@ -0,0 +1 @@
+1	Geslacht	M	male	V	female

diff --git a/test_data/test_data_NGS/dropzone/alternative/clinic/RDP-Patient_codebook.txt.sha1 b/test_data/test_data_NGS/dropzone/alternative/clinic/RDP-Patient_codebook.txt.sha1
@@ -0,0 +1 @@
+7854a94ee9adb8f765a65db17cd17fcc9fea708d  RDP-Patient_codebook.txt
diff --git a/...ropzone/full_dataset/NGS/pmc_test1.maf.gz → ...one/full_dataset/NGS/pmc_test1_WGS.maf.gz b/...ropzone/full_dataset/NGS/pmc_test1.maf.gz → ...one/full_dataset/NGS/pmc_test1_WGS.maf.gz
diff --git a/...ne/full_dataset/NGS/pmc_test1.maf.gz.sha1 → ...ull_dataset/NGS/pmc_test1_WGS.maf.gz.sha1 b/...ne/full_dataset/NGS/pmc_test1.maf.gz.sha1 → ...ull_dataset/NGS/pmc_test1_WGS.maf.gz.sha1
diff --git a/...ropzone/full_dataset/NGS/pmc_test2.maf.gz → ...one/full_dataset/NGS/pmc_test2_WGS.maf.gz b/...ropzone/full_dataset/NGS/pmc_test2.maf.gz → ...one/full_dataset/NGS/pmc_test2_WGS.maf.gz
diff --git a/...ne/full_dataset/NGS/pmc_test2.maf.gz.sha1 → ...ull_dataset/NGS/pmc_test2_WGS.maf.gz.sha1 b/...ne/full_dataset/NGS/pmc_test2.maf.gz.sha1 → ...ull_dataset/NGS/pmc_test2_WGS.maf.gz.sha1
diff --git a/...GS/dropzone/full_dataset/NGS/pmc_test.seg → ...ropzone/full_dataset/NGS/pmc_test_WXS.seg b/...GS/dropzone/full_dataset/NGS/pmc_test.seg → ...ropzone/full_dataset/NGS/pmc_test_WXS.seg
diff --git a/...opzone/full_dataset/NGS/pmc_test.seg.sha1 → ...ne/full_dataset/NGS/pmc_test_WXS.seg.sha1 b/...opzone/full_dataset/NGS/pmc_test.seg.sha1 → ...ne/full_dataset/NGS/pmc_test_WXS.seg.sha1
diff --git a/...ataset/NGS/pmc_test_all_data_by_genes.txt → ...et/NGS/pmc_test_WXS_all_data_by_genes.txt b/...ataset/NGS/pmc_test_all_data_by_genes.txt → ...et/NGS/pmc_test_WXS_all_data_by_genes.txt
diff --git a/...t/NGS/pmc_test_all_data_by_genes.txt.sha1 → ...S/pmc_test_WXS_all_data_by_genes.txt.sha1 b/...t/NGS/pmc_test_all_data_by_genes.txt.sha1 → ...S/pmc_test_WXS_all_data_by_genes.txt.sha1
diff --git a/...NGS/pmc_test_all_thresholded.by_genes.txt → ...pmc_test_WXS_all_thresholded.by_genes.txt b/...NGS/pmc_test_all_thresholded.by_genes.txt → ...pmc_test_WXS_all_thresholded.by_genes.txt
diff --git a/...mc_test_all_thresholded.by_genes.txt.sha1 → ...est_WXS_all_thresholded.by_genes.txt.sha1 b/...mc_test_all_thresholded.by_genes.txt.sha1 → ...est_WXS_all_thresholded.by_genes.txt.sha1
diff --git a/test_data/test_data_NGS/dropzone/full_dataset/clinic/RDP-Patient_codebook.txt b/test_data/test_data_NGS/dropzone/full_dataset/clinic/RDP-Patient_codebook.txt
@@ -0,0 +1 @@
+1	Geslacht	M	male	V	female

diff --git a/test_data/test_data_NGS/dropzone/full_dataset/clinic/RDP-Patient_codebook.txt.sha1 b/test_data/test_data_NGS/dropzone/full_dataset/clinic/RDP-Patient_codebook.txt.sha1
@@ -0,0 +1 @@
+7854a94ee9adb8f765a65db17cd17fcc9fea708d  RDP-Patient_codebook.txt
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		7854a94ee9adb8f765a65db17cd17fcc9fea708d RDP-Patient_codebook.txt