HallLab · AndreRico · Nov 14, 2023 · Nov 15, 2023 · Nov 15, 2023 · Jun 4, 2024
diff --git a/.gitignore b/.gitignore
diff --git a/.vscode/launch.json b/.vscode/launch.json
@@ -14,6 +14,33 @@
             ],
             "django": true
         },
+        {
+            "name": "Django: Position to Term Map",
+            "type": "python",
+            "request": "launch",
+            "program": "${workspaceFolder}/igem/manage.py",
+            "args": [
+                "filter",
+                "--positions",
+                // "/Users/andrerico/DEV/projects/igem/IGEM_SandBox/scripts/echo/echo_genes_prod/output_files/10301_sch_gxe_0.7.txt",
+                // "/Users/andrerico/DEV/projects/igem/IGEM_SandBox/scripts/echo/echo_genes_prod/output_files/10701_sch_gxe_0.7.txt",
+                // "/Users/andrerico/DEV/projects/igem/IGEM_SandBox/scripts/echo/echo_genes_prod/output_files/11601_sch_gxe_0.7.txt",
+                // "/Users/andrerico/DEV/projects/igem/IGEM_SandBox/scripts/echo/echo_genes_prod/output_files/11901_affy5_sch_gxe_0.7.txt",
+                // "/Users/andrerico/DEV/projects/igem/IGEM_SandBox/scripts/echo/echo_genes_prod/output_files/11901_affy6_sch_gxe_0.7.txt",
+                // "/Users/andrerico/DEV/projects/igem/IGEM_SandBox/scripts/echo/echo_genes_prod/output_files/12801_sch_gxe_0.7.txt",
+                // "/Users/andrerico/DEV/projects/igem/IGEM_SandBox/scripts/echo/echo_genes_prod/output_files/10701_pre_gxe_0.7.txt",
+                // "/Users/andrerico/DEV/projects/igem/IGEM_SandBox/scripts/echo/echo_genes_prod/output_files/11901_affy5_pre_gxe_0.7.txt",
+                // "/Users/andrerico/DEV/projects/igem/IGEM_SandBox/scripts/echo/echo_genes_prod/output_files/11901_affy6_pre_gxe_0.7.txt",
+                "/Users/andrerico/DEV/projects/igem/IGEM_Support/scripts/echo/echo_genes_prod/output_files/12801_pre_gxe_0.7.txt",
+                "--exposome",
+                "/Users/andrerico/DEV/projects/igem/IGEM_Support/scripts/echo/echo_genes_prod/output_files/pre_echo_words_clean.csv",
+                "--assembly=37",
+                "--boundaries=10000",
+                "--delimiter=\\t"  // Use two backslashes to escape the tab character
+            ],
+            "django": true,
+            "console": "integratedTerminal"
+        }
         // {
         //     "type": "R-Debugger",
         //     "name": "Launch R-Workspace",

diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -24,7 +24,7 @@
       "editor.formatOnSave": true,
       "editor.formatOnType": true,
       "editor.codeActionsOnSave": {
-        "source.organizeImports": true
+        "source.organizeImports": "explicit"
       }
     },
     "[html]": {

diff --git a/AUTHORS.rst b/AUTHORS.rst
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
diff --git a/README.txt b/README.txt
diff --git a/dist/igem-0.1.0-py3-none-any.whl b/dist/igem-0.1.0-py3-none-any.whl
diff --git a/dist/igem-0.1.0.tar.gz b/dist/igem-0.1.0.tar.gz
diff --git a/dist/igem-0.1.1-py3-none-any.whl b/dist/igem-0.1.1-py3-none-any.whl
diff --git a/dist/igem-0.1.1.tar.gz b/dist/igem-0.1.1.tar.gz
diff --git a/dist/igem-0.1.2-py3-none-any.whl b/dist/igem-0.1.2-py3-none-any.whl
diff --git a/dist/igem-0.1.2.tar.gz b/dist/igem-0.1.2.tar.gz
diff --git a/dist/igem-0.1.3-py3-none-any.whl b/dist/igem-0.1.3-py3-none-any.whl
diff --git a/dist/igem-0.1.3.tar.gz b/dist/igem-0.1.3.tar.gz
diff --git a/dist/igem-0.1.4-py3-none-any.whl b/dist/igem-0.1.4-py3-none-any.whl
diff --git a/dist/igem-0.1.4.tar.gz b/dist/igem-0.1.4.tar.gz
diff --git a/dist/igem-0.1.4/LICENSE b/dist/igem-0.1.4/LICENSE
diff --git a/dist/igem-0.1.4/PKG-INFO b/dist/igem-0.1.4/PKG-INFO
diff --git a/dist/igem-0.1.4/README.txt b/dist/igem-0.1.4/README.txt
diff --git a/dist/igem-0.1.4/igem/__init__.py b/dist/igem-0.1.4/igem/__init__.py
diff --git a/dist/igem-0.1.4/igem/base_static/global/css/styles.css b/dist/igem-0.1.4/igem/base_static/global/css/styles.css
diff --git a/dist/igem-0.1.4/igem/base_static/global/js/scripts.js b/dist/igem-0.1.4/igem/base_static/global/js/scripts.js
diff --git a/dist/igem-0.1.4/igem/base_templates/global/base.html b/dist/igem-0.1.4/igem/base_templates/global/base.html
diff --git a/dist/igem-0.1.4/igem/base_templates/global/partials/footer.html b/dist/igem-0.1.4/igem/base_templates/global/partials/footer.html
diff --git a/dist/igem-0.1.4/igem/base_templates/global/partials/form.html b/dist/igem-0.1.4/igem/base_templates/global/partials/form.html
diff --git a/dist/igem-0.1.4/igem/base_templates/global/partials/head.html b/dist/igem-0.1.4/igem/base_templates/global/partials/head.html
diff --git a/dist/igem-0.1.4/igem/base_templates/global/partials/header.html b/dist/igem-0.1.4/igem/base_templates/global/partials/header.html
diff --git a/dist/igem-0.1.4/igem/base_templates/global/partials/menu.html b/dist/igem-0.1.4/igem/base_templates/global/partials/menu.html
diff --git a/dist/igem-0.1.4/igem/base_templates/global/partials/messages.html b/dist/igem-0.1.4/igem/base_templates/global/partials/messages.html
diff --git a/dist/igem-0.1.4/igem/base_templates/global/partials/pagination.html b/dist/igem-0.1.4/igem/base_templates/global/partials/pagination.html
diff --git a/dist/igem-0.1.4/igem/base_templates/global/partials/search.html b/dist/igem-0.1.4/igem/base_templates/global/partials/search.html
diff --git a/dist/igem-0.1.4/igem/epc/__init__.py b/dist/igem-0.1.4/igem/epc/__init__.py
diff --git a/dist/igem-0.1.4/igem/epc/clarite/analyze/__init__.py b/dist/igem-0.1.4/igem/epc/clarite/analyze/__init__.py
diff --git a/dist/igem-0.1.4/igem/epc/clarite/analyze/analyze.py b/dist/igem-0.1.4/igem/epc/clarite/analyze/analyze.py
diff --git a/dist/igem-0.1.4/igem/epc/clarite/analyze/interaction.py b/dist/igem-0.1.4/igem/epc/clarite/analyze/interaction.py
diff --git a/dist/igem-0.1.4/igem/epc/clarite/describe/__init__.py b/dist/igem-0.1.4/igem/epc/clarite/describe/__init__.py
diff --git a/dist/igem-0.1.4/igem/epc/clarite/describe/describe.py b/dist/igem-0.1.4/igem/epc/clarite/describe/describe.py
diff --git a/dist/igem-0.1.4/igem/epc/clarite/load/__init__.py b/dist/igem-0.1.4/igem/epc/clarite/load/__init__.py
diff --git a/dist/igem-0.1.4/igem/epc/clarite/load/load.py b/dist/igem-0.1.4/igem/epc/clarite/load/load.py
diff --git a/dist/igem-0.1.4/igem/epc/clarite/modify/__init__.py b/dist/igem-0.1.4/igem/epc/clarite/modify/__init__.py
diff --git a/dist/igem-0.1.4/igem/epc/clarite/modify/modify.py b/dist/igem-0.1.4/igem/epc/clarite/modify/modify.py
diff --git a/dist/igem-0.1.4/igem/epc/clarite/plot/__init__.py b/dist/igem-0.1.4/igem/epc/clarite/plot/__init__.py
diff --git a/dist/igem-0.1.4/igem/epc/clarite/plot/plot.py b/dist/igem-0.1.4/igem/epc/clarite/plot/plot.py
diff --git a/dist/igem-0.1.4/igem/epc/clarite/survey/__init__.py b/dist/igem-0.1.4/igem/epc/clarite/survey/__init__.py
diff --git a/dist/igem-0.1.4/igem/epc/clarite/survey/survey.py b/dist/igem-0.1.4/igem/epc/clarite/survey/survey.py
diff --git a/dist/igem-0.1.4/igem/epc/tests/py_test_output/.gitignore b/dist/igem-0.1.4/igem/epc/tests/py_test_output/.gitignore
diff --git a/dist/igem-0.1.4/igem/epc/tests/py_test_output/top_results_nhanesreal.png b/dist/igem-0.1.4/igem/epc/tests/py_test_output/top_results_nhanesreal.png
diff --git a/dist/igem-0.1.4/igem/epc/tests/py_test_output/top_results_nhanesreal_no_cutoff.png b/dist/igem-0.1.4/igem/epc/tests/py_test_output/top_results_nhanesreal_no_cutoff.png
diff --git a/dist/igem-0.1.4/igem/epc/tests/py_test_output/top_results_nhanessmall.png b/dist/igem-0.1.4/igem/epc/tests/py_test_output/top_results_nhanessmall.png
diff --git a/dist/igem-0.1.4/igem/epc/tests/test_analyze/conftest.py b/dist/igem-0.1.4/igem/epc/tests/test_analyze/conftest.py
diff --git a/dist/igem-0.1.4/igem/epc/tests/test_analyze/test_association_study.py b/dist/igem-0.1.4/igem/epc/tests/test_analyze/test_association_study.py
diff --git a/dist/igem-0.1.4/igem/epc/tests/test_analyze/test_exe_pairwise.py b/dist/igem-0.1.4/igem/epc/tests/test_analyze/test_exe_pairwise.py
diff --git a/dist/igem-0.1.4/igem/epc/tests/test_analyze/test_gwas.py b/dist/igem-0.1.4/igem/epc/tests/test_analyze/test_gwas.py
diff --git a/dist/igem-0.1.4/igem/epc/tests/test_analyze/test_interaction_study.py b/dist/igem-0.1.4/igem/epc/tests/test_analyze/test_interaction_study.py
diff --git a/dist/igem-0.1.4/igem/epc/tests/test_describe/conftest.py b/dist/igem-0.1.4/igem/epc/tests/test_describe/conftest.py
diff --git a/dist/igem-0.1.4/igem/epc/tests/test_describe/test_describe.py b/dist/igem-0.1.4/igem/epc/tests/test_describe/test_describe.py
diff --git a/dist/igem-0.1.4/igem/epc/tests/test_load/test_load.py b/dist/igem-0.1.4/igem/epc/tests/test_load/test_load.py
diff --git a/dist/igem-0.1.4/igem/epc/tests/test_modify/conftest.py b/dist/igem-0.1.4/igem/epc/tests/test_modify/conftest.py
diff --git a/dist/igem-0.1.4/igem/epc/tests/test_modify/test_modify.py b/dist/igem-0.1.4/igem/epc/tests/test_modify/test_modify.py
diff --git a/dist/igem-0.1.4/igem/epc/tests/test_plot/conftest.py b/dist/igem-0.1.4/igem/epc/tests/test_plot/conftest.py
diff --git a/dist/igem-0.1.4/igem/epc/tests/test_plot/test_plot.py b/dist/igem-0.1.4/igem/epc/tests/test_plot/test_plot.py
diff --git a/dist/igem-0.1.4/igem/ge/admin.py b/dist/igem-0.1.4/igem/ge/admin.py
diff --git a/dist/igem-0.1.4/igem/ge/apps.py b/dist/igem-0.1.4/igem/ge/apps.py
diff --git a/dist/igem-0.1.4/igem/ge/db/__init__.py b/dist/igem-0.1.4/igem/ge/db/__init__.py
diff --git a/dist/igem-0.1.4/igem/ge/db/get.py b/dist/igem-0.1.4/igem/ge/db/get.py
diff --git a/dist/igem-0.1.4/igem/ge/db/sync.py b/dist/igem-0.1.4/igem/ge/db/sync.py
diff --git a/dist/igem-0.1.4/igem/ge/filter/__init__.py b/dist/igem-0.1.4/igem/ge/filter/__init__.py
diff --git a/dist/igem-0.1.4/igem/ge/filter/convert.py b/dist/igem-0.1.4/igem/ge/filter/convert.py
diff --git a/dist/igem-0.1.4/igem/ge/filter/filters.py b/dist/igem-0.1.4/igem/ge/filter/filters.py
diff --git a/dist/igem-0.1.4/igem/ge/filter/tag.py b/dist/igem-0.1.4/igem/ge/filter/tag.py
diff --git a/dist/igem-0.1.4/igem/ge/filter/utils.py b/dist/igem-0.1.4/igem/ge/filter/utils.py
diff --git a/dist/igem-0.1.4/igem/ge/forms/__init__.py b/dist/igem-0.1.4/igem/ge/forms/__init__.py
diff --git a/dist/igem-0.1.4/igem/ge/forms/form_connector.py b/dist/igem-0.1.4/igem/ge/forms/form_connector.py
diff --git a/dist/igem-0.1.4/igem/ge/forms/form_wordterm.py b/dist/igem-0.1.4/igem/ge/forms/form_wordterm.py
diff --git a/dist/igem-0.1.4/igem/ge/management/commands/db.py b/dist/igem-0.1.4/igem/ge/management/commands/db.py
diff --git a/dist/igem-0.1.4/igem/ge/management/commands/filter.py b/dist/igem-0.1.4/igem/ge/management/commands/filter.py
diff --git a/dist/igem-0.1.4/igem/ge/management/commands/olds/collect.py b/dist/igem-0.1.4/igem/ge/management/commands/olds/collect.py
diff --git a/dist/igem-0.1.4/igem/ge/management/commands/olds/create_table.py b/dist/igem-0.1.4/igem/ge/management/commands/olds/create_table.py
diff --git a/dist/igem-0.1.4/igem/ge/management/commands/olds/db.py b/dist/igem-0.1.4/igem/ge/management/commands/olds/db.py
diff --git a/dist/igem-0.1.4/igem/ge/management/commands/olds/filter.py b/dist/igem-0.1.4/igem/ge/management/commands/olds/filter.py
diff --git a/dist/igem-0.1.4/igem/ge/management/commands/olds/filter_gene.py b/dist/igem-0.1.4/igem/ge/management/commands/olds/filter_gene.py
diff --git a/dist/igem-0.1.4/igem/ge/management/commands/olds/map.py b/dist/igem-0.1.4/igem/ge/management/commands/olds/map.py
diff --git a/dist/igem-0.1.4/igem/ge/management/commands/olds/prepare.py b/dist/igem-0.1.4/igem/ge/management/commands/olds/prepare.py
diff --git a/dist/igem-0.1.4/igem/ge/management/commands/olds/reduce.py b/dist/igem-0.1.4/igem/ge/management/commands/olds/reduce.py
diff --git a/dist/igem-0.1.4/igem/ge/migrations/0001_initial.py b/dist/igem-0.1.4/igem/ge/migrations/0001_initial.py
diff --git a/....1.4/igem/ge/migrations/0002_logs_delete_logscollector_wfcontrol_igem_version_and_more.py b/....1.4/igem/ge/migrations/0002_logs_delete_logscollector_wfcontrol_igem_version_and_more.py
diff --git a/...gem-0.1.4/igem/ge/migrations/0003_alter_logs_igem_version_alter_wfcontrol_igem_version.py b/...gem-0.1.4/igem/ge/migrations/0003_alter_logs_igem_version_alter_wfcontrol_igem_version.py
diff --git a/...gem-0.1.4/igem/ge/migrations/0004_alter_logs_igem_version_alter_wfcontrol_igem_version.py b/...gem-0.1.4/igem/ge/migrations/0004_alter_logs_igem_version_alter_wfcontrol_igem_version.py
diff --git a/dist/igem-0.1.4/igem/ge/migrations/0005_alter_wfcontrol_status.py b/dist/igem-0.1.4/igem/ge/migrations/0005_alter_wfcontrol_status.py
diff --git a/...gem-0.1.4/igem/ge/migrations/0006_alter_logs_igem_version_alter_wfcontrol_igem_version.py b/...gem-0.1.4/igem/ge/migrations/0006_alter_logs_igem_version_alter_wfcontrol_igem_version.py
diff --git a/dist/igem-0.1.4/igem/ge/models.py b/dist/igem-0.1.4/igem/ge/models.py
diff --git a/dist/igem-0.1.4/igem/ge/templates/ge/pages/detailview_connector.html b/dist/igem-0.1.4/igem/ge/templates/ge/pages/detailview_connector.html
diff --git a/dist/igem-0.1.4/igem/ge/templates/ge/pages/detailview_wordterm.html b/dist/igem-0.1.4/igem/ge/templates/ge/pages/detailview_wordterm.html
diff --git a/dist/igem-0.1.4/igem/ge/templates/ge/pages/listview_connector.html b/dist/igem-0.1.4/igem/ge/templates/ge/pages/listview_connector.html
diff --git a/dist/igem-0.1.4/igem/ge/templates/ge/pages/listview_wordterm.html b/dist/igem-0.1.4/igem/ge/templates/ge/pages/listview_wordterm.html
diff --git a/dist/igem-0.1.4/igem/ge/templates/ge/partials/login_message.html b/dist/igem-0.1.4/igem/ge/templates/ge/partials/login_message.html
diff --git a/dist/igem-0.1.4/igem/ge/tests/test_base.py b/dist/igem-0.1.4/igem/ge/tests/test_base.py
diff --git a/dist/igem-0.1.4/igem/ge/tests/test_db.py b/dist/igem-0.1.4/igem/ge/tests/test_db.py
diff --git a/dist/igem-0.1.4/igem/ge/tests/test_filter.py b/dist/igem-0.1.4/igem/ge/tests/test_filter.py
diff --git a/dist/igem-0.1.4/igem/ge/tests/test_model.py b/dist/igem-0.1.4/igem/ge/tests/test_model.py
diff --git a/dist/igem-0.1.4/igem/ge/tests/test_tag.py b/dist/igem-0.1.4/igem/ge/tests/test_tag.py
diff --git a/dist/igem-0.1.4/igem/ge/urls.py b/dist/igem-0.1.4/igem/ge/urls.py
diff --git a/dist/igem-0.1.4/igem/ge/utils/__init__.py b/dist/igem-0.1.4/igem/ge/utils/__init__.py
diff --git a/dist/igem-0.1.4/igem/ge/utils/logs.py b/dist/igem-0.1.4/igem/ge/utils/logs.py
diff --git a/dist/igem-0.1.4/igem/ge/views.py b/dist/igem-0.1.4/igem/ge/views.py
diff --git a/dist/igem-0.1.4/igem/ge/views/__init__.py b/dist/igem-0.1.4/igem/ge/views/__init__.py
diff --git a/dist/igem-0.1.4/igem/ge/views/detailview_connector.py b/dist/igem-0.1.4/igem/ge/views/detailview_connector.py
diff --git a/dist/igem-0.1.4/igem/ge/views/detailview_wordterm.py b/dist/igem-0.1.4/igem/ge/views/detailview_wordterm.py
diff --git a/dist/igem-0.1.4/igem/ge/views/listviews_all.py b/dist/igem-0.1.4/igem/ge/views/listviews_all.py
diff --git a/dist/igem-0.1.4/igem/omics/admin.py b/dist/igem-0.1.4/igem/omics/admin.py
diff --git a/dist/igem-0.1.4/igem/omics/apps.py b/dist/igem-0.1.4/igem/omics/apps.py
diff --git a/dist/igem-0.1.4/igem/omics/db/__init__.py b/dist/igem-0.1.4/igem/omics/db/__init__.py
diff --git a/dist/igem-0.1.4/igem/omics/db/dbSNP_XML_CSV.py b/dist/igem-0.1.4/igem/omics/db/dbSNP_XML_CSV.py
diff --git a/dist/igem-0.1.4/igem/omics/db/get.py b/dist/igem-0.1.4/igem/omics/db/get.py
diff --git a/dist/igem-0.1.4/igem/omics/db/load.py b/dist/igem-0.1.4/igem/omics/db/load.py
diff --git a/dist/igem-0.1.4/igem/omics/management/commands/omics.py b/dist/igem-0.1.4/igem/omics/management/commands/omics.py
diff --git a/dist/igem-0.1.4/igem/omics/migrations/0001_initial.py b/dist/igem-0.1.4/igem/omics/migrations/0001_initial.py
diff --git a/dist/igem-0.1.4/igem/omics/models.py b/dist/igem-0.1.4/igem/omics/models.py
diff --git a/dist/igem-0.1.4/igem/omics/tests/test_ncbi.py b/dist/igem-0.1.4/igem/omics/tests/test_ncbi.py
diff --git a/dist/igem-0.1.4/igem/omics/views.py b/dist/igem-0.1.4/igem/omics/views.py
diff --git a/dist/igem-0.1.4/igem/server/admin.py b/dist/igem-0.1.4/igem/server/admin.py
diff --git a/dist/igem-0.1.4/igem/server/apps.py b/dist/igem-0.1.4/igem/server/apps.py
diff --git a/dist/igem-0.1.4/igem/server/etl/__init__.py b/dist/igem-0.1.4/igem/server/etl/__init__.py
diff --git a/dist/igem-0.1.4/igem/server/etl/collect.py b/dist/igem-0.1.4/igem/server/etl/collect.py
diff --git a/dist/igem-0.1.4/igem/server/etl/extractors.py b/dist/igem-0.1.4/igem/server/etl/extractors.py
diff --git a/dist/igem-0.1.4/igem/server/etl/map.py b/dist/igem-0.1.4/igem/server/etl/map.py
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