├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE.txt ├── README.md ├── __init__.py ├── example ├── config-example.yaml └── genbanks │ ├── GCF_000005845.2.gbff.gz │ ├── GCF_000008865.2.gbff.gz │ └── GCF_000407825.1.gbff.gz ├── multismash ├── __init__.py ├── multismash.py └── multismash_config.py ├── pyproject.toml └── workflow ├── Snakefile ├── __init__.py ├── config └── config-template.yaml ├── envs └── bigscape.yaml ├── rules └── common.smk ├── schema └── config.schema.yaml └── scripts ├── __init__.py ├── count_regions.py ├── tabulate_regions.py └── test ├── __init__.py ├── test_count_regions.py └── test_tabulate_regions.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/README.md -------------------------------------------------------------------------------- /__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /example/config-example.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/example/config-example.yaml -------------------------------------------------------------------------------- /example/genbanks/GCF_000005845.2.gbff.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/example/genbanks/GCF_000005845.2.gbff.gz -------------------------------------------------------------------------------- /example/genbanks/GCF_000008865.2.gbff.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/example/genbanks/GCF_000008865.2.gbff.gz -------------------------------------------------------------------------------- /example/genbanks/GCF_000407825.1.gbff.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/example/genbanks/GCF_000407825.1.gbff.gz -------------------------------------------------------------------------------- /multismash/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /multismash/multismash.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/multismash/multismash.py -------------------------------------------------------------------------------- /multismash/multismash_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/multismash/multismash_config.py -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/pyproject.toml -------------------------------------------------------------------------------- /workflow/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/workflow/Snakefile -------------------------------------------------------------------------------- /workflow/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /workflow/config/config-template.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/workflow/config/config-template.yaml -------------------------------------------------------------------------------- /workflow/envs/bigscape.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/workflow/envs/bigscape.yaml -------------------------------------------------------------------------------- /workflow/rules/common.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/workflow/rules/common.smk -------------------------------------------------------------------------------- /workflow/schema/config.schema.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/workflow/schema/config.schema.yaml -------------------------------------------------------------------------------- /workflow/scripts/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /workflow/scripts/count_regions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/workflow/scripts/count_regions.py -------------------------------------------------------------------------------- /workflow/scripts/tabulate_regions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/workflow/scripts/tabulate_regions.py -------------------------------------------------------------------------------- /workflow/scripts/test/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /workflow/scripts/test/test_count_regions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/workflow/scripts/test/test_count_regions.py -------------------------------------------------------------------------------- /workflow/scripts/test/test_tabulate_regions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zreitz/multismash/HEAD/workflow/scripts/test/test_tabulate_regions.py --------------------------------------------------------------------------------