LICENSE
MANIFEST.in
README.md
requirements.txt
setup.cfg
setup.py
./onkopus/onkopus
onkopus/__init__.py
onkopus/__main__.py
onkopus/import_data.py
onkopus/mtb_requests.py
onkopus/onkopus_main.py
onkopus.egg-info/PKG-INFO
onkopus.egg-info/SOURCES.txt
onkopus.egg-info/dependency_links.txt
onkopus.egg-info/requires.txt
onkopus.egg-info/top_level.txt
onkopus/conf/__init__.py
onkopus/conf/config.ini
onkopus/conf/docker_config.py
onkopus/conf/read_config.py
onkopus/onkopus_clients/__init__.py
onkopus/onkopus_clients/aggregator_client.py
onkopus/onkopus_clients/biomarker_recognition_client.py
onkopus/onkopus_clients/ccs_gene_fusion_client.py
onkopus/onkopus_clients/ccs_genomic_client.py
onkopus/onkopus_clients/ccs_liftover_client.py
onkopus/onkopus_clients/civic_client.py
onkopus/onkopus_clients/clinvar_client.py
onkopus/onkopus_clients/dbnsfp_client.py
onkopus/onkopus_clients/dbsnp_client.py
onkopus/onkopus_clients/drugclass_client.py
onkopus/onkopus_clients/fathmm_client.py
onkopus/onkopus_clients/loftool_client.py
onkopus/onkopus_clients/metakb_client.py
onkopus/onkopus_clients/mvp_client.py
onkopus/onkopus_clients/oncokb_client.py
onkopus/onkopus_clients/primateai_client.py
onkopus/onkopus_clients/revel_client.py
onkopus/onkopus_clients/uta_adapter_client.py
onkopus/onkopus_clients/vuspredict_client.py
onkopus/onkopus_clients/aggregated_clients/__init__.py
onkopus/onkopus_clients/aggregated_clients/all_modules_client.py
onkopus/onkopus_clients/aggregated_clients/clinsig_client.py
onkopus/onkopus_clients/aggregated_clients/pathogenicity_client.py
onkopus/onkopus_clients/data_import/__init__.py
onkopus/onkopus_clients/data_import/import_data.py
onkopus/onkopus_clients/processing/__init__.py
onkopus/onkopus_clients/processing/parse_json.py
onkopus/onkopus_clients/single_module_clients/__init__.py
onkopus/onkopus_clients/single_module_clients/alpha_missense_client.py
onkopus/onkopus_clients/single_module_clients/civic_gene_client.py
onkopus/onkopus_clients/single_module_clients/civic_nearby_client.py
onkopus/onkopus_clients/single_module_clients/cosmic_genecensus_client.py
onkopus/onkopus_clients/single_module_clients/default_features_client.py
onkopus/onkopus_clients/single_module_clients/dgidb_client.py
onkopus/onkopus_clients/single_module_clients/ge_client.py
onkopus/onkopus_clients/single_module_clients/ge_plot_client.py
onkopus/onkopus_clients/single_module_clients/gencode_client.py
onkopus/onkopus_clients/single_module_clients/gencode_gene_name_client.py
onkopus/onkopus_clients/single_module_clients/gencode_genomic_client.py
onkopus/onkopus_clients/single_module_clients/gencode_mane_select_transcript_client.py
onkopus/onkopus_clients/single_module_clients/interpreter_client.py
onkopus/onkopus_clients/single_module_clients/molecular_features_client.py
onkopus/onkopus_clients/single_module_clients/onkopus_server_client.py
onkopus/onkopus_clients/single_module_clients/pdb_client.py
onkopus/onkopus_clients/single_module_clients/plot_client.py
onkopus/onkopus_clients/single_module_clients/protein_feature_client.py
onkopus/onkopus_clients/single_module_clients/scannet_client.py
onkopus/onkopus_clients/single_module_clients/uta_adapter_protein_sequence_client.py
onkopus/onkopus_writer/__init__.py
onkopus/onkopus_writer/clinsig_tsv_writer.py
onkopus/plot/__init__.py
onkopus/plot/generate_plot_graph_data.py
onkopus/plot/protein_features_plot.py
onkopus/processing/__init__.py
onkopus/processing/annotate.py
onkopus/processing/annotate_variants.py
onkopus/processing/fusion_request.py
onkopus/processing/gene_request.py
onkopus/processing/indel_request.py
onkopus/processing/parallel_gene_requests.py
onkopus/processing/parallel_requests.py
onkopus/processing/snv_request.py
onkopus/processing/threads.py
onkopus/remote/__init__.py
onkopus/remote/upload_config.ini
onkopus/tools/__init__.py
onkopus/tools/biomarker_types.py
onkopus/tools/file_types.py
onkopus/tools/io.py
onkopus/transform/ProteinToGenomic.py
onkopus/transform/__init__.py
tests/__init__.py
tests/test_multiprocess_annotation.py
tests/test_annotation/__init__.py
tests/test_annotation/test_annotation_clients.py
tests/test_annotation/test_annotation_multiple_types.py
tests/test_annotation/test_full_annotation.py
tests/test_annotation/test_gene_annotation.py
tests/test_annotation/test_indel_annotation.py
tests/test_annotation/test_snv_annotation.py
tests/test_annotation/test_stream_based_annotation.py
tests/test_annotation/test_stream_based_annotation_all_modules.py
tests/test_annotation/test_custom_annotation/__init__.py
tests/test_annotation/test_custom_annotation/test_vcf.py
tests/test_biomarker_types/__init__.py
tests/test_biomarker_types/test_split_by_mutation_type.py
tests/test_cli/__init__.py
tests/test_cli/test_cli_annotation.py
tests/test_io/__init__.py
tests/test_io/test_csv_annotation.py
tests/test_io/test_read_annotated_data.py
tests/test_io/test_specific_features_export.py
tests/test_io/test_treatment_export.py
tests/test_io/test_variant_avf_export.py
tests/test_io/test_variant_data_export.py
tests/test_io/test_variant_vcf_export.py
tests/test_io/test_write_annotated_data.py
tests/test_onkopus_clients/__init__.py
tests/test_onkopus_clients/test_file_based_onkopus_annotation.py
tests/test_onkopus_clients/test_onkopus_io_functions.py
tests/test_onkopus_clients/test_single_onkopus_clients/__init__.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_aggregation_client.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_alphamissense.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_blosum_client.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_civic.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_civic_gene_client.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_clinvar.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_cosmic_gene_census.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_dbnsfp.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_dbsnp.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_dgidb_gene_client.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_drugclass.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_ge_client.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_ge_plot_client.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_gencode.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_gencode_gene_name.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_gencode_genomic.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_gencode_mane_select_transcript.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_get_drug_classes.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_interpreter_client.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_liftover.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_loftool.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_metakb.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_molecular_features_client.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_mvp.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_oncokb.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_onkopus_server_client.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_plots.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_preprocessing.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_primateai.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_protein_feature_client.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_protein_pdb_client.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_revel.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_scannet_client.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_uta-adapter.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_uta-adapter_fusion.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_uta-adapter_gene.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_uta_adapter_protein_sequence.py
tests/test_onkopus_clients/test_single_onkopus_clients/test_vuspredict_client.py
tests/test_tools/__init__.py
tests/test_tools/test_alternate_allele_filtering.py
tests/test_tools/test_biomarker_type_conversion.py
tests/test_transformations/__init__.py
tests/test_transformations/test_protein_to_genomic.py