Remove database generation from main function (#21)

vanallenlab · Jul 12, 2024 · 10561af · 10561af
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diff --git a/moalmanac/datasources/README.md → datasources/README.md b/moalmanac/datasources/README.md → datasources/README.md
diff --git a/moalmanac/datasources/acmg/README.md → datasources/acmg/README.md b/moalmanac/datasources/acmg/README.md → datasources/acmg/README.md
diff --git a/...ources/acmg/acmg.secondaryfindings.v3.txt → ...ources/acmg/acmg.secondaryfindings.v3.txt b/...ources/acmg/acmg.secondaryfindings.v3.txt → ...ources/acmg/acmg.secondaryfindings.v3.txt
diff --git a/...ac/datasources/cancergenecensus/README.md → datasources/cancergenecensus/README.md b/...ac/datasources/cancergenecensus/README.md → datasources/cancergenecensus/README.md
diff --git a/...necensus/cancer_gene_census_v97.genes.tsv → ...necensus/cancer_gene_census_v97.genes.tsv b/...necensus/cancer_gene_census_v97.genes.tsv → ...necensus/cancer_gene_census_v97.genes.tsv
diff --git a/...sources/cancergenecensus/diff_versions.py → ...sources/cancergenecensus/diff_versions.py b/...sources/cancergenecensus/diff_versions.py → ...sources/cancergenecensus/diff_versions.py
diff --git a/...sources/cancergenecensus/extract_genes.py → ...sources/cancergenecensus/extract_genes.py b/...sources/cancergenecensus/extract_genes.py → ...sources/cancergenecensus/extract_genes.py
diff --git a/...anac/datasources/cancerhotspots/README.md → datasources/cancerhotspots/README.md b/...anac/datasources/cancerhotspots/README.md → datasources/cancerhotspots/README.md
diff --git a/...c/datasources/cancerhotspots/hotspots.txt → datasources/cancerhotspots/hotspots.txt b/...c/datasources/cancerhotspots/hotspots.txt → datasources/cancerhotspots/hotspots.txt
diff --git a/...datasources/cancerhotspots/hotspots3d.txt → datasources/cancerhotspots/hotspots3d.txt b/...datasources/cancerhotspots/hotspots3d.txt → datasources/cancerhotspots/hotspots3d.txt
diff --git a/...atasources/cancerhotspots/hotspots_v2.txt → datasources/cancerhotspots/hotspots_v2.txt b/...atasources/cancerhotspots/hotspots_v2.txt → datasources/cancerhotspots/hotspots_v2.txt
diff --git a/...rhotspots/prep_3dhotspots/3d_hotspots.xls → ...rhotspots/prep_3dhotspots/3d_hotspots.xls b/...rhotspots/prep_3dhotspots/3d_hotspots.xls → ...rhotspots/prep_3dhotspots/3d_hotspots.xls
diff --git a/...tspots/prep_3dhotspots/3d_hotspots_T2.txt → ...tspots/prep_3dhotspots/3d_hotspots_T2.txt b/...tspots/prep_3dhotspots/3d_hotspots_T2.txt → ...tspots/prep_3dhotspots/3d_hotspots_T2.txt
diff --git a/...tspots/prep_3dhotspots/3d_hotspots_T5.txt → ...tspots/prep_3dhotspots/3d_hotspots_T5.txt b/...tspots/prep_3dhotspots/3d_hotspots_T5.txt → ...tspots/prep_3dhotspots/3d_hotspots_T5.txt
diff --git a/...otspots/prep_3dhotspots/prep3dhotspots.py → ...otspots/prep_3dhotspots/prep3dhotspots.py b/...otspots/prep_3dhotspots/prep3dhotspots.py → ...otspots/prep_3dhotspots/prep3dhotspots.py
diff --git a/moalmanac/datasources/clinvar/README.md → datasources/clinvar/README.md b/moalmanac/datasources/clinvar/README.md → datasources/clinvar/README.md
diff --git a/...ac/datasources/clinvar/prepare_clinvar.py → datasources/clinvar/prepare_clinvar.py b/...ac/datasources/clinvar/prepare_clinvar.py → datasources/clinvar/prepare_clinvar.py
diff --git a/...asources/clinvar/variant_summary.lite.txt → datasources/clinvar/variant_summary.lite.txt b/...asources/clinvar/variant_summary.lite.txt → datasources/clinvar/variant_summary.lite.txt
diff --git a/moalmanac/datasources/cosmic/README.md → datasources/cosmic/README.md b/moalmanac/datasources/cosmic/README.md → datasources/cosmic/README.md
diff --git a/...anac/datasources/cosmic/prepare_cosmic.py → datasources/cosmic/prepare_cosmic.py b/...anac/datasources/cosmic/prepare_cosmic.py → datasources/cosmic/prepare_cosmic.py
diff --git a/moalmanac/datasources/exac/README.md → datasources/exac/README.md b/moalmanac/datasources/exac/README.md → datasources/exac/README.md
diff --git a/moalmanac/datasources/exac/build_exac.sh → datasources/exac/build_exac.sh b/moalmanac/datasources/exac/build_exac.sh → datasources/exac/build_exac.sh
diff --git a/moalmanac/datasources/exac/expand_exac.py → datasources/exac/expand_exac.py b/moalmanac/datasources/exac/expand_exac.py → datasources/exac/expand_exac.py
diff --git a/.../gsea_gene_sets/GSEA_cancer_gene_sets.txt → .../gsea_gene_sets/GSEA_cancer_gene_sets.txt b/.../gsea_gene_sets/GSEA_cancer_gene_sets.txt → .../gsea_gene_sets/GSEA_cancer_gene_sets.txt
diff --git a/...anac/datasources/gsea_gene_sets/README.md → datasources/gsea_gene_sets/README.md b/...anac/datasources/gsea_gene_sets/README.md → datasources/gsea_gene_sets/README.md
diff --git a/...ces/gsea_gene_sets/c4.cm.v6.0.symbols.txt → ...ces/gsea_gene_sets/c4.cm.v6.0.symbols.txt b/...ces/gsea_gene_sets/c4.cm.v6.0.symbols.txt → ...ces/gsea_gene_sets/c4.cm.v6.0.symbols.txt
diff --git a/moalmanac/datasources/hereditary/README.md → datasources/hereditary/README.md b/moalmanac/datasources/hereditary/README.md → datasources/hereditary/README.md
diff --git a/...nac/datasources/hereditary/hereditary.txt → datasources/hereditary/hereditary.txt b/...nac/datasources/hereditary/hereditary.txt → datasources/hereditary/hereditary.txt
diff --git a/moalmanac/datasources/lawrence/README.md → datasources/lawrence/README.md b/moalmanac/datasources/lawrence/README.md → datasources/lawrence/README.md
diff --git a/...nac/datasources/lawrence/lawrence_ST2.txt → datasources/lawrence/lawrence_ST2.txt b/...nac/datasources/lawrence/lawrence_ST2.txt → datasources/lawrence/lawrence_ST2.txt
diff --git a/...ces/lawrence/lawrence_mapped_ontology.txt → ...ces/lawrence/lawrence_mapped_ontology.txt b/...ces/lawrence/lawrence_mapped_ontology.txt → ...ces/lawrence/lawrence_mapped_ontology.txt
diff --git a/...rces/lawrence/map_oncotree_lawrence.ipynb → ...rces/lawrence/map_oncotree_lawrence.ipynb b/...rces/lawrence/map_oncotree_lawrence.ipynb → ...rces/lawrence/map_oncotree_lawrence.ipynb
diff --git a/moalmanac/datasources/moalmanac/README.md → datasources/moalmanac/README.md b/moalmanac/datasources/moalmanac/README.md → datasources/moalmanac/README.md
diff --git a/...atasources/moalmanac/create_almanac_db.py → datasources/moalmanac/create_almanac_db.py b/...atasources/moalmanac/create_almanac_db.py → datasources/moalmanac/create_almanac_db.py
diff --git a/...moalmanac/molecular-oncology-almanac.json → ...moalmanac/molecular-oncology-almanac.json b/...moalmanac/molecular-oncology-almanac.json → ...moalmanac/molecular-oncology-almanac.json
diff --git a/moalmanac/datasources/oncotree/README.md → datasources/oncotree/README.md b/moalmanac/datasources/oncotree/README.md → datasources/oncotree/README.md
diff --git a/...anac/datasources/oncotree/get_oncotree.py → datasources/oncotree/get_oncotree.py b/...anac/datasources/oncotree/get_oncotree.py → datasources/oncotree/get_oncotree.py
diff --git a/...asources/oncotree/oncotree.2023-03-09.txt → datasources/oncotree/oncotree.2023-03-09.txt b/...asources/oncotree/oncotree.2023-03-09.txt → datasources/oncotree/oncotree.2023-03-09.txt
diff --git a/moalmanac/datasources/preclinical/README.md → datasources/preclinical/README.md b/moalmanac/datasources/preclinical/README.md → datasources/preclinical/README.md
diff --git a/...es/preclinical/almanac-gdsc-mappings.json → ...es/preclinical/almanac-gdsc-mappings.json b/...es/preclinical/almanac-gdsc-mappings.json → ...es/preclinical/almanac-gdsc-mappings.json
diff --git a/...tasources/preclinical/annotated/README.md → datasources/preclinical/annotated/README.md b/...tasources/preclinical/annotated/README.md → datasources/preclinical/annotated/README.md
diff --git a/...inical/annotated/annotate-copy-numbers.py → ...inical/annotated/annotate-copy-numbers.py b/...inical/annotated/annotate-copy-numbers.py → ...inical/annotated/annotate-copy-numbers.py
diff --git a/...preclinical/annotated/annotate-fusions.py → ...preclinical/annotated/annotate-fusions.py b/...preclinical/annotated/annotate-fusions.py → ...preclinical/annotated/annotate-fusions.py
diff --git a/.../annotated/annotate-molecular-features.sh → .../annotated/annotate-molecular-features.sh b/.../annotated/annotate-molecular-features.sh → .../annotated/annotate-molecular-features.sh
diff --git a/...reclinical/annotated/annotate-variants.py → ...reclinical/annotated/annotate-variants.py b/...reclinical/annotated/annotate-variants.py → ...reclinical/annotated/annotate-variants.py
diff --git a/...ted/cell-lines.copy-numbers.annotated.txt → ...ted/cell-lines.copy-numbers.annotated.txt b/...ted/cell-lines.copy-numbers.annotated.txt → ...ted/cell-lines.copy-numbers.annotated.txt
diff --git a/...ed/cell-lines.fusions.annotated.gene1.txt → ...ed/cell-lines.fusions.annotated.gene1.txt b/...ed/cell-lines.fusions.annotated.gene1.txt → ...ed/cell-lines.fusions.annotated.gene1.txt
diff --git a/...ed/cell-lines.fusions.annotated.gene2.txt → ...ed/cell-lines.fusions.annotated.gene2.txt b/...ed/cell-lines.fusions.annotated.gene2.txt → ...ed/cell-lines.fusions.annotated.gene2.txt
diff --git a/...nnotated/cell-lines.fusions.annotated.txt → ...nnotated/cell-lines.fusions.annotated.txt b/...nnotated/cell-lines.fusions.annotated.txt → ...nnotated/cell-lines.fusions.annotated.txt
diff --git a/...cell-lines.somatic-variants.annotated.txt → ...cell-lines.somatic-variants.annotated.txt b/...cell-lines.somatic-variants.annotated.txt → ...cell-lines.somatic-variants.annotated.txt
diff --git a/...ac/datasources/preclinical/cell-lines.pkl → datasources/preclinical/cell-lines.pkl b/...ac/datasources/preclinical/cell-lines.pkl → datasources/preclinical/cell-lines.pkl
diff --git a/...cal/formatted/0.map-almanac-to-gdsc.ipynb → ...cal/formatted/0.map-almanac-to-gdsc.ipynb b/...cal/formatted/0.map-almanac-to-gdsc.ipynb → ...cal/formatted/0.map-almanac-to-gdsc.ipynb
diff --git a/...rocess-cell-line-molecular-features.ipynb → ...rocess-cell-line-molecular-features.ipynb b/...rocess-cell-line-molecular-features.ipynb → ...rocess-cell-line-molecular-features.ipynb
diff --git a/...tasources/preclinical/formatted/README.md → datasources/preclinical/formatted/README.md b/...tasources/preclinical/formatted/README.md → datasources/preclinical/formatted/README.md
diff --git a/...ical/formatted/almanac-gdsc-mappings.json → ...ical/formatted/almanac-gdsc-mappings.json b/...ical/formatted/almanac-gdsc-mappings.json → ...ical/formatted/almanac-gdsc-mappings.json
diff --git a/...l/formatted/cell-line-names.formatted.txt → ...l/formatted/cell-line-names.formatted.txt b/...l/formatted/cell-line-names.formatted.txt → ...l/formatted/cell-line-names.formatted.txt
diff --git a/...cal/formatted/cell-lines.copy-numbers.txt → ...cal/formatted/cell-lines.copy-numbers.txt b/...cal/formatted/cell-lines.copy-numbers.txt → ...cal/formatted/cell-lines.copy-numbers.txt
diff --git a/...clinical/formatted/cell-lines.fusions.txt → ...clinical/formatted/cell-lines.fusions.txt b/...clinical/formatted/cell-lines.fusions.txt → ...clinical/formatted/cell-lines.fusions.txt
diff --git a/...formatted/cell-lines.somatic-variants.txt → ...formatted/cell-lines.somatic-variants.txt b/...formatted/cell-lines.somatic-variants.txt → ...formatted/cell-lines.somatic-variants.txt
diff --git a/...clinical/formatted/cell-lines.summary.txt → ...clinical/formatted/cell-lines.summary.txt b/...clinical/formatted/cell-lines.summary.txt → ...clinical/formatted/cell-lines.summary.txt
diff --git a/...ces/preclinical/formatted/sanger.gdsc.txt → ...ces/preclinical/formatted/sanger.gdsc.txt b/...ces/preclinical/formatted/sanger.gdsc.txt → ...ces/preclinical/formatted/sanger.gdsc.txt
diff --git a/...ces/preclinical/generate-dictionary.ipynb → ...ces/preclinical/generate-dictionary.ipynb b/...ces/preclinical/generate-dictionary.ipynb → ...ces/preclinical/generate-dictionary.ipynb
diff --git a/.../datasources/preclinical/source/README.md → datasources/preclinical/source/README.md b/.../datasources/preclinical/source/README.md → datasources/preclinical/source/README.md
diff --git a/...es/preclinical/source/ccle-2019/README.md → ...es/preclinical/source/ccle-2019/README.md b/...es/preclinical/source/ccle-2019/README.md → ...es/preclinical/source/ccle-2019/README.md
diff --git a/...urces/preclinical/source/depmap/README.md → ...urces/preclinical/source/depmap/README.md b/...urces/preclinical/source/depmap/README.md → ...urces/preclinical/source/depmap/README.md
diff --git a/...sources/preclinical/source/gdsc/README.md → ...sources/preclinical/source/gdsc/README.md b/...sources/preclinical/source/gdsc/README.md → ...sources/preclinical/source/gdsc/README.md
diff --git a/example_output/example_output.actionable.txt b/example_output/example_output.actionable.txt
diff --git a/moalmanac/README.md b/moalmanac/README.md
diff --git a/moalmanac/annotation-databases.ini b/moalmanac/annotation-databases.ini
diff --git a/moalmanac/annotator.py b/moalmanac/annotator.py
diff --git a/moalmanac/config.ini b/moalmanac/config.ini
diff --git a/moalmanac/config.py b/moalmanac/config.py
diff --git a/moalmanac/datasources.py b/moalmanac/datasources.py
diff --git a/moalmanac/evaluator.py b/moalmanac/evaluator.py
diff --git a/moalmanac/features.py b/moalmanac/features.py
diff --git a/moalmanac/illustrator.py b/moalmanac/illustrator.py
diff --git a/moalmanac/investigator.py b/moalmanac/investigator.py
diff --git a/moalmanac/matchmaker.py b/moalmanac/matchmaker.py
diff --git a/moalmanac/moalmanac.py b/moalmanac/moalmanac.py
diff --git a/moalmanac/preclinical-databases.ini b/moalmanac/preclinical-databases.ini
diff --git a/moalmanac/reader.py b/moalmanac/reader.py
diff --git a/moalmanac/reporter.py b/moalmanac/reporter.py
diff --git a/moalmanac/run_deconstructsigs.R b/moalmanac/run_deconstructsigs.R
diff --git a/moalmanac/run_example.py b/moalmanac/run_example.py
diff --git a/moalmanac/simplified_input.py b/moalmanac/simplified_input.py
diff --git a/moalmanac/test/README.md b/moalmanac/test/README.md
diff --git a/moalmanac/test/annotator_tests.py b/moalmanac/test/annotator_tests.py
diff --git a/moalmanac/test/datasources_tests.py b/moalmanac/test/datasources_tests.py
diff --git a/moalmanac/test/evaluator_tests.py b/moalmanac/test/evaluator_tests.py
diff --git a/moalmanac/test/features_tests.py b/moalmanac/test/features_tests.py
diff --git a/moalmanac/test/investigator_tests.py b/moalmanac/test/investigator_tests.py
diff --git a/moalmanac/wrapper_deconstructsigs.sh b/moalmanac/wrapper_deconstructsigs.sh