Remove database generation from main function #21

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Merged

brendanreardon merged 19 commits into main from remove_database_generation_from_main

Jul 12, 2024

0 moalmanac/datasources/README.md → datasources/README.md

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0 moalmanac/datasources/acmg/README.md → datasources/acmg/README.md

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0 ...ources/acmg/acmg.secondaryfindings.v3.txt → ...ources/acmg/acmg.secondaryfindings.v3.txt

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0 ...ac/datasources/cancergenecensus/README.md → datasources/cancergenecensus/README.md

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0 ...necensus/cancer_gene_census_v97.genes.tsv → ...necensus/cancer_gene_census_v97.genes.tsv

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0 ...sources/cancergenecensus/diff_versions.py → ...sources/cancergenecensus/diff_versions.py

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0 ...sources/cancergenecensus/extract_genes.py → ...sources/cancergenecensus/extract_genes.py

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0 ...anac/datasources/cancerhotspots/README.md → datasources/cancerhotspots/README.md

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0 ...c/datasources/cancerhotspots/hotspots.txt → datasources/cancerhotspots/hotspots.txt

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0 ...datasources/cancerhotspots/hotspots3d.txt → datasources/cancerhotspots/hotspots3d.txt

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0 ...atasources/cancerhotspots/hotspots_v2.txt → datasources/cancerhotspots/hotspots_v2.txt

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...rhotspots/prep_3dhotspots/3d_hotspots.xls → ...rhotspots/prep_3dhotspots/3d_hotspots.xls

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0 ...tspots/prep_3dhotspots/3d_hotspots_T2.txt → ...tspots/prep_3dhotspots/3d_hotspots_T2.txt

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0 ...tspots/prep_3dhotspots/3d_hotspots_T5.txt → ...tspots/prep_3dhotspots/3d_hotspots_T5.txt

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0 ...otspots/prep_3dhotspots/prep3dhotspots.py → ...otspots/prep_3dhotspots/prep3dhotspots.py

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0 moalmanac/datasources/clinvar/README.md → datasources/clinvar/README.md

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0 ...ac/datasources/clinvar/prepare_clinvar.py → datasources/clinvar/prepare_clinvar.py

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0 ...asources/clinvar/variant_summary.lite.txt → datasources/clinvar/variant_summary.lite.txt

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0 moalmanac/datasources/cosmic/README.md → datasources/cosmic/README.md

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0 ...anac/datasources/cosmic/prepare_cosmic.py → datasources/cosmic/prepare_cosmic.py

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0 moalmanac/datasources/exac/README.md → datasources/exac/README.md

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0 moalmanac/datasources/exac/build_exac.sh → datasources/exac/build_exac.sh

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0 moalmanac/datasources/exac/expand_exac.py → datasources/exac/expand_exac.py

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0 .../gsea_gene_sets/GSEA_cancer_gene_sets.txt → .../gsea_gene_sets/GSEA_cancer_gene_sets.txt

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0 ...anac/datasources/gsea_gene_sets/README.md → datasources/gsea_gene_sets/README.md

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0 ...ces/gsea_gene_sets/c4.cm.v6.0.symbols.txt → ...ces/gsea_gene_sets/c4.cm.v6.0.symbols.txt

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0 moalmanac/datasources/hereditary/README.md → datasources/hereditary/README.md

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0 ...nac/datasources/hereditary/hereditary.txt → datasources/hereditary/hereditary.txt

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0 moalmanac/datasources/lawrence/README.md → datasources/lawrence/README.md

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0 ...nac/datasources/lawrence/lawrence_ST2.txt → datasources/lawrence/lawrence_ST2.txt

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0 ...ces/lawrence/lawrence_mapped_ontology.txt → ...ces/lawrence/lawrence_mapped_ontology.txt

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0 ...rces/lawrence/map_oncotree_lawrence.ipynb → ...rces/lawrence/map_oncotree_lawrence.ipynb

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0 moalmanac/datasources/moalmanac/README.md → datasources/moalmanac/README.md

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0 ...atasources/moalmanac/create_almanac_db.py → datasources/moalmanac/create_almanac_db.py

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0 ...moalmanac/molecular-oncology-almanac.json → ...moalmanac/molecular-oncology-almanac.json

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0 moalmanac/datasources/oncotree/README.md → datasources/oncotree/README.md

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0 ...anac/datasources/oncotree/get_oncotree.py → datasources/oncotree/get_oncotree.py

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0 ...asources/oncotree/oncotree.2023-03-09.txt → datasources/oncotree/oncotree.2023-03-09.txt

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0 moalmanac/datasources/preclinical/README.md → datasources/preclinical/README.md

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0 ...es/preclinical/almanac-gdsc-mappings.json → ...es/preclinical/almanac-gdsc-mappings.json

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0 ...tasources/preclinical/annotated/README.md → datasources/preclinical/annotated/README.md

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0 ...inical/annotated/annotate-copy-numbers.py → ...inical/annotated/annotate-copy-numbers.py

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0 ...preclinical/annotated/annotate-fusions.py → ...preclinical/annotated/annotate-fusions.py

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0 .../annotated/annotate-molecular-features.sh → .../annotated/annotate-molecular-features.sh

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0 ...reclinical/annotated/annotate-variants.py → ...reclinical/annotated/annotate-variants.py

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0 ...ted/cell-lines.copy-numbers.annotated.txt → ...ted/cell-lines.copy-numbers.annotated.txt

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0 ...ed/cell-lines.fusions.annotated.gene1.txt → ...ed/cell-lines.fusions.annotated.gene1.txt

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0 ...ed/cell-lines.fusions.annotated.gene2.txt → ...ed/cell-lines.fusions.annotated.gene2.txt

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0 ...nnotated/cell-lines.fusions.annotated.txt → ...nnotated/cell-lines.fusions.annotated.txt

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0 ...cell-lines.somatic-variants.annotated.txt → ...cell-lines.somatic-variants.annotated.txt

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...ac/datasources/preclinical/cell-lines.pkl → datasources/preclinical/cell-lines.pkl

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0 ...cal/formatted/0.map-almanac-to-gdsc.ipynb → ...cal/formatted/0.map-almanac-to-gdsc.ipynb

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0 ...rocess-cell-line-molecular-features.ipynb → ...rocess-cell-line-molecular-features.ipynb

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0 ...tasources/preclinical/formatted/README.md → datasources/preclinical/formatted/README.md

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0 ...ical/formatted/almanac-gdsc-mappings.json → ...ical/formatted/almanac-gdsc-mappings.json

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0 ...l/formatted/cell-line-names.formatted.txt → ...l/formatted/cell-line-names.formatted.txt

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0 ...cal/formatted/cell-lines.copy-numbers.txt → ...cal/formatted/cell-lines.copy-numbers.txt

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0 ...clinical/formatted/cell-lines.fusions.txt → ...clinical/formatted/cell-lines.fusions.txt

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0 ...formatted/cell-lines.somatic-variants.txt → ...formatted/cell-lines.somatic-variants.txt

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0 ...clinical/formatted/cell-lines.summary.txt → ...clinical/formatted/cell-lines.summary.txt

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0 ...ces/preclinical/formatted/sanger.gdsc.txt → ...ces/preclinical/formatted/sanger.gdsc.txt

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0 ...ces/preclinical/generate-dictionary.ipynb → ...ces/preclinical/generate-dictionary.ipynb

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0 .../datasources/preclinical/source/README.md → datasources/preclinical/source/README.md

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0 ...es/preclinical/source/ccle-2019/README.md → ...es/preclinical/source/ccle-2019/README.md

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0 ...urces/preclinical/source/depmap/README.md → ...urces/preclinical/source/depmap/README.md

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0 ...sources/preclinical/source/gdsc/README.md → ...sources/preclinical/source/gdsc/README.md

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example_output/example_output.actionable.txt

moalmanac/README.md

moalmanac/annotation-databases.ini

moalmanac/annotator.py

moalmanac/config.ini

moalmanac/config.py

moalmanac/datasources.py

moalmanac/evaluator.py

moalmanac/features.py

moalmanac/illustrator.py

moalmanac/investigator.py

moalmanac/matchmaker.py

moalmanac/moalmanac.py

moalmanac/preclinical-databases.ini

moalmanac/reader.py

moalmanac/reporter.py

moalmanac/run_deconstructsigs.R

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moalmanac/run_example.py

moalmanac/simplified_input.py

moalmanac/test/README.md

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moalmanac/test/annotator_tests.py

moalmanac/test/datasources_tests.py

moalmanac/test/evaluator_tests.py

moalmanac/test/features_tests.py

moalmanac/test/investigator_tests.py

moalmanac/wrapper_deconstructsigs.sh

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