python-scripts/Pacini-typing
python-scripts/pacini_typing
site-packages/codon_table_enum.py
site-packages/command_utils.py
site-packages/config/O1.yaml
site-packages/config/O139.yaml
site-packages/config/VIB-O1.fasta
site-packages/config/VIB-O139.fasta
site-packages/config/Yersinia.yaml
site-packages/config/__init__.py
site-packages/config/accept_arguments.yaml
site-packages/handle_search_modes.py
site-packages/make_gene_database.py
site-packages/make_snp_database.py
site-packages/pacini_typing-3.0.1.dist-info/INSTALLER
site-packages/pacini_typing-3.0.1.dist-info/METADATA
site-packages/pacini_typing-3.0.1.dist-info/RECORD
site-packages/pacini_typing-3.0.1.dist-info/REQUESTED
site-packages/pacini_typing-3.0.1.dist-info/WHEEL
site-packages/pacini_typing-3.0.1.dist-info/direct_url.json
site-packages/pacini_typing-3.0.1.dist-info/entry_points.txt
site-packages/pacini_typing-3.0.1.dist-info/licenses/LICENSE
site-packages/pacini_typing-3.0.1.dist-info/top_level.txt
site-packages/pacini_typing.py
site-packages/parsing/__init__.py
site-packages/parsing/alignment_extractor.py
site-packages/parsing/coverage_filter.py
site-packages/parsing/fasta_parser.py
site-packages/parsing/fastq_parser.py
site-packages/parsing/filter_pattern.py
site-packages/parsing/identity_filter.py
site-packages/parsing/parser.py
site-packages/parsing/parsing_manager.py
site-packages/parsing/parsing_strategy.py
site-packages/parsing/read_config_pattern.py
site-packages/parsing/snp_parser.py
site-packages/preprocessing/__init__.py
site-packages/preprocessing/argsparse/__init__.py
site-packages/preprocessing/argsparse/args_makedatabase.py
site-packages/preprocessing/argsparse/args_query.py
site-packages/preprocessing/argsparse/build_parser.py
site-packages/preprocessing/exceptions/__init__.py
site-packages/preprocessing/exceptions/alignment_exceptions.py
site-packages/preprocessing/exceptions/command_utils_exceptions.py
site-packages/preprocessing/exceptions/determine_input_type_exceptions.py
site-packages/preprocessing/exceptions/parsing_exceptions.py
site-packages/preprocessing/exceptions/snp_detection_exceptions.py
site-packages/preprocessing/exceptions/validate_database_exceptions.py
site-packages/preprocessing/exceptions/validation_exceptions.py
site-packages/preprocessing/validation/__init__.py
site-packages/preprocessing/validation/determine_input_type.py
site-packages/preprocessing/validation/validate_database.py
site-packages/preprocessing/validation/validate_pointfinder_database.py
site-packages/preprocessing/validation/validating_input_arguments.py
site-packages/queries/__init__.py
site-packages/queries/base_query_runner.py
site-packages/queries/blast_runner.py
site-packages/queries/gene_query_runner.py
site-packages/queries/kma_runner.py
site-packages/queries/pointfinder_runner.py
site-packages/queries/query_runners.py
site-packages/queries/snp_query_runnner.py
site-packages/tests/__init__.py
site-packages/tests/e2e/__init__.py
site-packages/tests/e2e/check_tool_existence.py
site-packages/tests/e2e/test_end2end_config.py
site-packages/tests/e2e/test_end2end_makedatabase.py
site-packages/tests/e2e/test_end2end_non_paired_run.py
site-packages/tests/e2e/test_end2end_paired_run.py
site-packages/tests/test_alignment_extractor.py
site-packages/tests/test_command_utils.py
site-packages/tests/test_determine_input_type.py
site-packages/tests/test_raising_exceptions.py
site-packages/tests/test_read_config_pattern.py
site-packages/tests/test_runners.py
site-packages/tests/test_validate_database.py
site-packages/tests/test_validating_input_arguments.py
