├── .gitignore ├── .travis.yml ├── AUTHORS ├── CHANGELOG.md ├── Dockerfile ├── LICENSE ├── README.md ├── _config.yml ├── example_data ├── README ├── final_public_version.embl ├── input.gff └── output_to_be_submitted.embl ├── gff3toembl ├── EMBLContig.py ├── EMBLConverter.py ├── EMBLWriter.py ├── VisitorStream.py ├── __init__.py └── tests │ ├── EMBLContig_test.py │ ├── EMBLConverter_test.py │ ├── EMBLWriter_test.py │ └── data │ ├── chromosome_list.gff │ ├── chromosome_list_plasmid_name.gff │ ├── duplicate_coords.gff │ ├── expected_chromosome_list.txt │ ├── expected_chromosome_list_plasmid_name.txt │ ├── expected_duplicate_coords.embl │ ├── expected_large_annotation.embl │ ├── expected_single_feature.embl │ ├── expected_single_feature_new_locus_tag.embl │ ├── expected_single_feature_translation_table.embl │ ├── first_feature_missing.gff │ ├── large_annotation.gff │ └── single_feature.gff ├── install_dependencies.sh ├── paper.bib ├── paper.md ├── scripts └── gff3_to_embl └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/.travis.yml -------------------------------------------------------------------------------- /AUTHORS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/AUTHORS -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/README.md -------------------------------------------------------------------------------- /_config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/_config.yml -------------------------------------------------------------------------------- /example_data/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/example_data/README -------------------------------------------------------------------------------- /example_data/final_public_version.embl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/example_data/final_public_version.embl -------------------------------------------------------------------------------- /example_data/input.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/example_data/input.gff -------------------------------------------------------------------------------- /example_data/output_to_be_submitted.embl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/example_data/output_to_be_submitted.embl -------------------------------------------------------------------------------- /gff3toembl/EMBLContig.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/EMBLContig.py -------------------------------------------------------------------------------- /gff3toembl/EMBLConverter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/EMBLConverter.py -------------------------------------------------------------------------------- /gff3toembl/EMBLWriter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/EMBLWriter.py -------------------------------------------------------------------------------- /gff3toembl/VisitorStream.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/VisitorStream.py -------------------------------------------------------------------------------- /gff3toembl/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /gff3toembl/tests/EMBLContig_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/EMBLContig_test.py -------------------------------------------------------------------------------- /gff3toembl/tests/EMBLConverter_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/EMBLConverter_test.py -------------------------------------------------------------------------------- /gff3toembl/tests/EMBLWriter_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/EMBLWriter_test.py -------------------------------------------------------------------------------- /gff3toembl/tests/data/chromosome_list.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/data/chromosome_list.gff -------------------------------------------------------------------------------- /gff3toembl/tests/data/chromosome_list_plasmid_name.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/data/chromosome_list_plasmid_name.gff -------------------------------------------------------------------------------- /gff3toembl/tests/data/duplicate_coords.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/data/duplicate_coords.gff -------------------------------------------------------------------------------- /gff3toembl/tests/data/expected_chromosome_list.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/data/expected_chromosome_list.txt -------------------------------------------------------------------------------- /gff3toembl/tests/data/expected_chromosome_list_plasmid_name.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/data/expected_chromosome_list_plasmid_name.txt -------------------------------------------------------------------------------- /gff3toembl/tests/data/expected_duplicate_coords.embl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/data/expected_duplicate_coords.embl -------------------------------------------------------------------------------- /gff3toembl/tests/data/expected_large_annotation.embl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/data/expected_large_annotation.embl -------------------------------------------------------------------------------- /gff3toembl/tests/data/expected_single_feature.embl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/data/expected_single_feature.embl -------------------------------------------------------------------------------- /gff3toembl/tests/data/expected_single_feature_new_locus_tag.embl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/data/expected_single_feature_new_locus_tag.embl -------------------------------------------------------------------------------- /gff3toembl/tests/data/expected_single_feature_translation_table.embl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/data/expected_single_feature_translation_table.embl -------------------------------------------------------------------------------- /gff3toembl/tests/data/first_feature_missing.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/data/first_feature_missing.gff -------------------------------------------------------------------------------- /gff3toembl/tests/data/large_annotation.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/data/large_annotation.gff -------------------------------------------------------------------------------- /gff3toembl/tests/data/single_feature.gff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/gff3toembl/tests/data/single_feature.gff -------------------------------------------------------------------------------- /install_dependencies.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/install_dependencies.sh -------------------------------------------------------------------------------- /paper.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/paper.bib -------------------------------------------------------------------------------- /paper.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/paper.md -------------------------------------------------------------------------------- /scripts/gff3_to_embl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/scripts/gff3_to_embl -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sanger-pathogens/gff3toembl/HEAD/setup.py --------------------------------------------------------------------------------