.codacy.yaml
CHANGELOG.md
LICENSE.txt
MANIFEST.in
README.md
conda-enviroment.yaml
pyproject.toml
requirements.txt
setup.cfg
pgatk/__init__.py
pgatk/cli.py
pgatk.egg-info/PKG-INFO
pgatk.egg-info/SOURCES.txt
pgatk.egg-info/dependency_links.txt
pgatk.egg-info/entry_points.txt
pgatk.egg-info/not-zip-safe
pgatk.egg-info/requires.txt
pgatk.egg-info/top_level.txt
pgatk/cgenomes/__init__.py
pgatk/cgenomes/cbioportal_downloader.py
pgatk/cgenomes/cgenomes_proteindb.py
pgatk/cgenomes/cosmic_downloader.py
pgatk/cgenomes/models.py
pgatk/clinvar/__init__.py
pgatk/clinvar/chromosome_mapper.py
pgatk/clinvar/clinvar_service.py
pgatk/clinvar/data_downloader.py
pgatk/commands/__init__.py
pgatk/commands/blast_get_position.py
pgatk/commands/cbioportal_downloader.py
pgatk/commands/cbioportal_to_proteindb.py
pgatk/commands/clinvar_to_proteindb.py
pgatk/commands/cosmic_downloader.py
pgatk/commands/cosmic_to_proteindb.py
pgatk/commands/digest_mutant_protein.py
pgatk/commands/dnaseq_to_proteindb.py
pgatk/commands/ensembl_database.py
pgatk/commands/ensembl_downloader.py
pgatk/commands/gencode_downloader.py
pgatk/commands/gnomad_vcf_downloader.py
pgatk/commands/map_peptide2genome.py
pgatk/commands/ncbi_downloader.py
pgatk/commands/proteindb_decoy.py
pgatk/commands/threeframe_translation.py
pgatk/commands/utils.py
pgatk/commands/validate_peptides.py
pgatk/commands/vcf_to_proteindb.py
pgatk/config/__init__.py
pgatk/config/assemblies_conf.json
pgatk/config/cbioportal_config.yaml
pgatk/config/clinvar_config.yaml
pgatk/config/cosmic_config.yaml
pgatk/config/ensembl_config.yaml
pgatk/config/ensembl_downloader_config.yaml
pgatk/config/protein_decoy.yaml
pgatk/config/registry.py
pgatk/db/__init__.py
pgatk/db/digest_mutant_protein.py
pgatk/db/map_peptide2genome.py
pgatk/ensembl/__init__.py
pgatk/ensembl/data_downloader.py
pgatk/ensembl/ensembl.py
pgatk/ensembl/exceptions.py
pgatk/ensembl/models.py
pgatk/gnomad/__init__.py
pgatk/gnomad/data_downloader.py
pgatk/proteogenomics/__init__.py
pgatk/proteogenomics/blast_get_position.py
pgatk/proteogenomics/spectrumai.py
pgatk/proteomics/__init__.py
pgatk/proteomics/models.py
pgatk/proteomics/db/__init__.py
pgatk/proteomics/db/protein_database_decoy.py
pgatk/toolbox/__init__.py
pgatk/toolbox/exceptions.py
pgatk/toolbox/general.py
pgatk/toolbox/rest.py
pgatk/toolbox/vcf_utils.py