├── .gitignore ├── .travis.yml ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── examples ├── exac_head.vcf ├── minimal.vcf ├── small_vep.vcf ├── test_vcf.vcf └── test_vcf.vcf.gz ├── setup.cfg ├── setup.py ├── tests ├── __init__.py ├── test_build_compounds.py ├── test_build_info.py ├── test_build_models.py ├── test_build_vep_dict.py ├── test_build_vep_string.py ├── test_format_variant.py ├── test_genotype.py ├── test_get_rank_scores.py ├── test_header_parser.py ├── test_split_genotype.py ├── test_split_variants.py └── test_vcf_parser.py └── vcf_parser ├── __init__.py ├── cli ├── __init__.py └── command_line.py ├── genotype.py ├── header_parser.py ├── log.py ├── parser.py └── utils ├── __init__.py ├── build_compounds.py ├── build_info.py ├── build_models.py ├── build_vep.py ├── check_info.py ├── format_variant.py ├── rank_scores.py ├── split_genotype.py └── split_variants.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/.travis.yml -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/README.md -------------------------------------------------------------------------------- /examples/exac_head.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/examples/exac_head.vcf -------------------------------------------------------------------------------- /examples/minimal.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/examples/minimal.vcf -------------------------------------------------------------------------------- /examples/small_vep.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/examples/small_vep.vcf -------------------------------------------------------------------------------- /examples/test_vcf.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/examples/test_vcf.vcf -------------------------------------------------------------------------------- /examples/test_vcf.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/examples/test_vcf.vcf.gz -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [metadata] 2 | description-file = README.md -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/setup.py -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/test_build_compounds.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/tests/test_build_compounds.py -------------------------------------------------------------------------------- /tests/test_build_info.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/tests/test_build_info.py -------------------------------------------------------------------------------- /tests/test_build_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/tests/test_build_models.py -------------------------------------------------------------------------------- /tests/test_build_vep_dict.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/tests/test_build_vep_dict.py -------------------------------------------------------------------------------- /tests/test_build_vep_string.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/tests/test_build_vep_string.py -------------------------------------------------------------------------------- /tests/test_format_variant.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/tests/test_format_variant.py -------------------------------------------------------------------------------- /tests/test_genotype.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/tests/test_genotype.py -------------------------------------------------------------------------------- /tests/test_get_rank_scores.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/tests/test_get_rank_scores.py -------------------------------------------------------------------------------- /tests/test_header_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/tests/test_header_parser.py -------------------------------------------------------------------------------- /tests/test_split_genotype.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/tests/test_split_genotype.py -------------------------------------------------------------------------------- /tests/test_split_variants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/tests/test_split_variants.py -------------------------------------------------------------------------------- /tests/test_vcf_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/tests/test_vcf_parser.py -------------------------------------------------------------------------------- /vcf_parser/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/__init__.py -------------------------------------------------------------------------------- /vcf_parser/cli/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /vcf_parser/cli/command_line.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/cli/command_line.py -------------------------------------------------------------------------------- /vcf_parser/genotype.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/genotype.py -------------------------------------------------------------------------------- /vcf_parser/header_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/header_parser.py -------------------------------------------------------------------------------- /vcf_parser/log.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/log.py -------------------------------------------------------------------------------- /vcf_parser/parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/parser.py -------------------------------------------------------------------------------- /vcf_parser/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/utils/__init__.py -------------------------------------------------------------------------------- /vcf_parser/utils/build_compounds.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/utils/build_compounds.py -------------------------------------------------------------------------------- /vcf_parser/utils/build_info.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/utils/build_info.py -------------------------------------------------------------------------------- /vcf_parser/utils/build_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/utils/build_models.py -------------------------------------------------------------------------------- /vcf_parser/utils/build_vep.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/utils/build_vep.py -------------------------------------------------------------------------------- /vcf_parser/utils/check_info.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/utils/check_info.py -------------------------------------------------------------------------------- /vcf_parser/utils/format_variant.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/utils/format_variant.py -------------------------------------------------------------------------------- /vcf_parser/utils/rank_scores.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/utils/rank_scores.py -------------------------------------------------------------------------------- /vcf_parser/utils/split_genotype.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/utils/split_genotype.py -------------------------------------------------------------------------------- /vcf_parser/utils/split_variants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/moonso/vcf_parser/HEAD/vcf_parser/utils/split_variants.py --------------------------------------------------------------------------------