.gitignore
LICENSE
MANIFEST.in
NOTICE
README.md
conftest.py
mkdocs.yml
pyproject.toml
setup.py
.github/dependabot.yml
.github/actions/python_build/action.yml
.github/workflows/notice.yml
.github/workflows/publish.yml
cicd/gitlab/dot.gitlab-ci.yml
cicd/gitlab/parts/debug.gitlab-ci.yml
cicd/gitlab/parts/dockerbuild.genomio.gitlab-ci.yml
cicd/gitlab/parts/flatfile.gitlab-ci.yml
cicd/gitlab/parts/license.gitlab-ci.yml
cicd/gitlab/parts/perl.gitlab-ci.yml
cicd/gitlab/parts/python.gitlab-ci.yml
cicd/runtime/.gitignore
cicd/scripts/check_flatfile.py
cicd/scripts/check_license.py
cicd/templates/license_header.tpl
cicd/templates/notice.tpl
config/external_db_map/default.txt
config/external_db_map/minimal.txt
config/gff_metaparser/metaparser.conf
config/gff_metaparser/valid_structures.conf
config/gff_metaparser/metaparser/brc4.patch
config/gff_metaparser/metaparser/cds_with_parent_id.patch
config/gff_metaparser/metaparser/cncb_hgdc.conf
config/gff_metaparser/metaparser/flybase.conf
config/gff_metaparser/metaparser/ids2display.conf
config/gff_metaparser/metaparser/mgnify_prodig.conf
config/gff_metaparser/metaparser/no_protein_id.patch
config/gff_metaparser/metaparser/noxref.patch
config/gff_metaparser/metaparser/old_refseq_brc4.conf
config/gff_metaparser/metaparser/regions_no_syns.patch
config/gff_metaparser/metaparser/xref2gene.patch
config/gff_metaparser/valid_structures/test_pre_mirna.conf
config/gff_metaparser/valid_structures/test_sub.conf
containers/docker/genomio/Dockerfile
data/test/exon_cds_duplicated_ids_test.gff3
data/test/gene_cds_test.gff3
data/test/pre_mirna_test.gff3
data/test/sub_rule_test.gff3
data/test/circular_transspliced_feature/mt.fna
data/test/circular_transspliced_feature/pep.faa
data/test/circular_transspliced_feature/seq_region.json
data/test/circular_transspliced_feature/tidy.gff3
data/test/modules/download_asm_data/output/GCA_017607445.1_ASM1760744v1_assembly_report.txt
data/test/modules/download_asm_data/output/GCA_017607445.1_ASM1760744v1_genomic.fna.gz
data/test/modules/download_asm_data/output/GCA_017607445.1_ASM1760744v1_genomic.gbff.gz
data/test/modules/download_asm_data/output/GCA_017607445.1_ASM1760744v1_genomic.gff.gz
data/test/modules/download_asm_data/output/GCA_017607445.1_ASM1760744v1_protein.faa.gz
data/test/modules/download_genbank/output/output.gb
data/test/pipelines/dumper/db_factory_dbs.json
data/test/pipelines/dumper/dump_files/downloaded_ncbi_stats.json
data/test/pipelines/dumper/dump_files/dumped_core_stats.json
data/test/pipelines/dumper/dump_files/dumped_dna.fasta
data/test/pipelines/dumper/dump_files/dumped_genome.json
data/test/pipelines/dumper/dump_files/dumped_ids_events.tab
data/test/pipelines/dumper/dump_files/dumped_pep.fasta
data/test/pipelines/dumper/dump_files/dumped_seq_region.json
data/test/pipelines/dumper/dump_sql/dumped_db.sql.test
data/test/pipelines/genome_prepare/input_dir_brc_off/gen_prep_in_meta.json
data/test/pipelines/genome_prepare/input_dir_brc_on/gen_prep_in_meta.json
docs/BRC4_genome_compare_conf.md
docs/BRC4_genome_loader.md
docs/cicd_gitlab.md
docs/code_of_conduct.md
docs/genome_prepare.md
docs/index.md
docs/install.md
docs/nextflow.md
docs/pipelines.md
docs/trf_split_run.md
docs/usage.md
docs/img/ensembl-logo.png
docs/scripts/gen_ref_pages.py
docs/stylesheets/extra.css
pipelines/nextflow/README.md
pipelines/nextflow/log_template.md
pipelines/nextflow/template_meta.yml
pipelines/nextflow/modules/annotation/dump_annotation.nf
pipelines/nextflow/modules/database/db_factory.nf
pipelines/nextflow/modules/database/dump_db.nf
pipelines/nextflow/modules/download/datasets_genome_meta.nf
pipelines/nextflow/modules/download/download_asm_data.nf
pipelines/nextflow/modules/download/download_genbank.nf
pipelines/nextflow/modules/events/dump_events.nf
pipelines/nextflow/modules/fasta/dump_fasta_dna.nf
pipelines/nextflow/modules/fasta/dump_fasta_peptides.nf
pipelines/nextflow/modules/fasta/process_fasta_data.nf
pipelines/nextflow/modules/files/publish_output.nf
pipelines/nextflow/modules/files/publish_output_dump.nf
pipelines/nextflow/modules/genbank/extract_from_gb.nf
pipelines/nextflow/modules/genome_metadata/accession_metadata.nf
pipelines/nextflow/modules/genome_metadata/amend_genome_data.nf
pipelines/nextflow/modules/genome_metadata/dump_genome_meta.nf
pipelines/nextflow/modules/genome_metadata/prepare_genome_metadata.nf
pipelines/nextflow/modules/genome_stats/compare_genome_stats.nf
pipelines/nextflow/modules/genome_stats/dump_genome_stats.nf
pipelines/nextflow/modules/gff3/dump_gff3.nf
pipelines/nextflow/modules/gff3/gff3_validation.nf
pipelines/nextflow/modules/gff3/process_gff3.nf
pipelines/nextflow/modules/gff3/unpack_gff3.nf
pipelines/nextflow/modules/manifest/integrity.nf
pipelines/nextflow/modules/manifest/manifest_maker.nf
pipelines/nextflow/modules/manifest/manifest_stats.nf
pipelines/nextflow/modules/schema/check_json_schema.nf
pipelines/nextflow/modules/schema/check_json_schema_db.nf
pipelines/nextflow/modules/schema/json_schema_factory.nf
pipelines/nextflow/modules/seq_region/dump_agp.nf
pipelines/nextflow/modules/seq_region/dump_seq_attrib.nf
pipelines/nextflow/modules/seq_region/dump_seq_regions.nf
pipelines/nextflow/modules/seq_region/process_seq_region.nf
pipelines/nextflow/modules/utils/utils.nf
pipelines/nextflow/subworkflows/yaml-schema.json
pipelines/nextflow/subworkflows/additional_seq_prepare/main.nf
pipelines/nextflow/subworkflows/additional_seq_prepare/meta.yml
pipelines/nextflow/subworkflows/dump_files/main.nf
pipelines/nextflow/subworkflows/dump_sql/main.nf
pipelines/nextflow/subworkflows/genome_prepare/main.nf
pipelines/nextflow/subworkflows/genome_prepare/meta.yml
pipelines/nextflow/tests/workflows/nextflow_test.config
pipelines/nextflow/tests/workflows/test_addition_prepare.yml
pipelines/nextflow/tests/workflows/test_dumper_files.yml
pipelines/nextflow/tests/workflows/test_dumper_sql.yml
pipelines/nextflow/tests/workflows/test_genome_prepare.yml
pipelines/nextflow/tests/workflows/test_genome_prepare_brc.yml
pipelines/nextflow/workflows/nextflow.config
pipelines/nextflow/workflows/additional_seq_prepare/main.nf
pipelines/nextflow/workflows/additional_seq_prepare/nextflow.config
pipelines/nextflow/workflows/additional_seq_prepare/nextflow_schema.json
pipelines/nextflow/workflows/conf/additional_seq_prepare-genomio.config
pipelines/nextflow/workflows/conf/dumper_pipeline-ensembllegacy.config
pipelines/nextflow/workflows/conf/dumper_pipeline-genomio.config
pipelines/nextflow/workflows/conf/genome_prepare-genomio.config
pipelines/nextflow/workflows/dumper_pipeline/README.md
pipelines/nextflow/workflows/dumper_pipeline/main.nf
pipelines/nextflow/workflows/dumper_pipeline/nextflow.config
pipelines/nextflow/workflows/dumper_pipeline/nextflow_schema.json
pipelines/nextflow/workflows/genome_prepare/main.nf
pipelines/nextflow/workflows/genome_prepare/nextflow.config
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scripts/README.md
scripts/get_dna_fasta_for.pl
scripts/load_fann.pl
scripts/trf_split_run.bash
scripts/gff_metaparser/gen_meta_conf.py
scripts/gff_metaparser/gff3_meta_parse.py
scripts/gff_metaparser/gff_stats.py
scripts/gff_metaparser/genmetaconf/__init__.py
scripts/gff_metaparser/genmetaconf/manifest.py
scripts/gff_metaparser/genmetaconf/metaconf.py
scripts/gff_metaparser/genmetaconf/seqregionconf.py
scripts/gff_metaparser/gffstruct/__init__.py
scripts/gff_metaparser/gffstruct/basekeeper.py
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scripts/gff_metaparser/gffstruct/fannkeeper.py
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scripts/gff_metaparser/gffstruct/prefixtree.py
scripts/gff_metaparser/gffstruct/seqfeatcomposer.py
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scripts/gff_metaparser/gffstruct/walkcontext.py
scripts/gff_metaparser/gffstruct/rules/__init__.py
scripts/gff_metaparser/gffstruct/rules/alias.py
scripts/gff_metaparser/gffstruct/rules/base.py
scripts/gff_metaparser/gffstruct/rules/fix.py
scripts/gff_metaparser/gffstruct/rules/fix_action.py
scripts/gff_metaparser/gffstruct/rules/gff.py
scripts/gff_metaparser/gffstruct/rules/ignore.py
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scripts/gff_metaparser/gffstruct/rules/unseen.py
scripts/gff_metaparser/gffstruct/rules/valid.py
scripts/stable_id_alloc/allocate_stable_ids.pl
scripts/stable_id_alloc/osid_add_organisms.py
scripts/stable_id_alloc/osid_check_organisms.py
src/containers/example.Dockerfile
src/perl/Bio/EnsEMBL/Pipeline/PipeConfig/BRC4_base_conf.pm
src/perl/Bio/EnsEMBL/Pipeline/PipeConfig/BRC4_genome_compare_conf.pm
src/perl/Bio/EnsEMBL/Pipeline/PipeConfig/BRC4_genome_loader_conf.pm
src/perl/Bio/EnsEMBL/Pipeline/PipeConfig/LoadGFF3Batch_conf.pm
src/perl/Bio/EnsEMBL/Pipeline/PipeConfig/LoadGFF3_conf.pm
src/perl/Bio/EnsEMBL/Pipeline/PipeConfig/README.md
src/perl/Bio/EnsEMBL/Pipeline/PipeConfig/gff3.ignore
src/perl/Bio/EnsEMBL/Pipeline/Runnable/BRC4/DbUrlToParams.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/BRC4/DumpFastaDNA.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/BRC4/DumpJsonBase.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/BRC4/DumpSeqRegionJson.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/BRC4/GetMetaValue.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/BRC4/ServerFromRegistry.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/AddSynonyms.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/AnalysisSetup.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/ApplySeqEdits.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/Base.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/ConstructFilenames.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/DeleteGenes.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/EmailReport.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/FixModels.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/LoadGFF3.pm
src/perl/Bio/EnsEMBL/Pipeline/Runnable/EG/LoadGFF3/ReportSeqEdits.pm
src/python/ensembl/brc4/__init__.py
src/python/ensembl/brc4/runnable/__init__.py
src/python/ensembl/brc4/runnable/compare_fasta.py
src/python/ensembl/brc4/runnable/compare_report.py
src/python/ensembl/brc4/runnable/fill_metadata.py
src/python/ensembl/brc4/runnable/json_schema_factory.py
src/python/ensembl/brc4/runnable/load_sequence_data.py
src/python/ensembl/brc4/runnable/prepare_genome.py
src/python/ensembl/brc4/runnable/seqregion_parser.py
src/python/ensembl/io/genomio/__init__.py
src/python/ensembl/io/genomio/annotation/__init__.py
src/python/ensembl/io/genomio/annotation/update_description.py
src/python/ensembl/io/genomio/assembly/__init__.py
src/python/ensembl/io/genomio/assembly/download.py
src/python/ensembl/io/genomio/assembly/status.py
src/python/ensembl/io/genomio/data/__init__.py
src/python/ensembl/io/genomio/data/external_db_map/__init__.py
src/python/ensembl/io/genomio/data/external_db_map/default.txt
src/python/ensembl/io/genomio/data/external_db_map/minimal.txt
src/python/ensembl/io/genomio/data/gff3/__init__.py
src/python/ensembl/io/genomio/data/gff3/biotypes.json
src/python/ensembl/io/genomio/data/schemas/__init__.py
src/python/ensembl/io/genomio/data/schemas/functional_annotation.json
src/python/ensembl/io/genomio/data/schemas/genome.json
src/python/ensembl/io/genomio/data/schemas/manifest.json
src/python/ensembl/io/genomio/data/schemas/seq_attrib.json
src/python/ensembl/io/genomio/data/schemas/seq_region.json
src/python/ensembl/io/genomio/database/__init__.py
src/python/ensembl/io/genomio/database/core_server.py
src/python/ensembl/io/genomio/database/dbconnection_lite.py
src/python/ensembl/io/genomio/database/factory.py
src/python/ensembl/io/genomio/database/meta_getter.py
src/python/ensembl/io/genomio/events/__init__.py
src/python/ensembl/io/genomio/events/dump.py
src/python/ensembl/io/genomio/events/format.py
src/python/ensembl/io/genomio/events/load.py
src/python/ensembl/io/genomio/external_db/__init__.py
src/python/ensembl/io/genomio/external_db/db_map.py
src/python/ensembl/io/genomio/fasta/__init__.py
src/python/ensembl/io/genomio/fasta/chunk.py
src/python/ensembl/io/genomio/fasta/compare.py
src/python/ensembl/io/genomio/fasta/process.py
src/python/ensembl/io/genomio/genbank/__init__.py
src/python/ensembl/io/genomio/genbank/download.py
src/python/ensembl/io/genomio/genbank/extract_data.py
src/python/ensembl/io/genomio/genome_metadata/__init__.py
src/python/ensembl/io/genomio/genome_metadata/dump.py
src/python/ensembl/io/genomio/genome_metadata/extend.py
src/python/ensembl/io/genomio/genome_metadata/prepare.py
src/python/ensembl/io/genomio/genome_stats/__init__.py
src/python/ensembl/io/genomio/genome_stats/compare.py
src/python/ensembl/io/genomio/genome_stats/dump.py
src/python/ensembl/io/genomio/gff3/__init__.py
src/python/ensembl/io/genomio/gff3/exceptions.py
src/python/ensembl/io/genomio/gff3/extract_annotation.py
src/python/ensembl/io/genomio/gff3/features.py
src/python/ensembl/io/genomio/gff3/gene_merger.py
src/python/ensembl/io/genomio/gff3/id_allocator.py
src/python/ensembl/io/genomio/gff3/overlaps.py
src/python/ensembl/io/genomio/gff3/process.py
src/python/ensembl/io/genomio/gff3/restructure.py
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src/python/ensembl/io/genomio/manifest/__init__.py
src/python/ensembl/io/genomio/manifest/check_integrity.py
src/python/ensembl/io/genomio/manifest/compute_stats.py
src/python/ensembl/io/genomio/manifest/generate.py
src/python/ensembl/io/genomio/manifest/manifest.py
src/python/ensembl/io/genomio/manifest/manifest_stats.py
src/python/ensembl/io/genomio/schemas/__init__.py
src/python/ensembl/io/genomio/schemas/json/__init__.py
src/python/ensembl/io/genomio/schemas/json/factory.py
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src/python/ensembl/io/genomio/seq_region/collection.py
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src/python/ensembl/io/genomio/seq_region/exceptions.py
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src/python/ensembl/io/genomio/seq_region/mappings.py
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src/python/ensembl/io/genomio/seq_region/report.py
src/python/ensembl/io/genomio/utils/__init__.py
src/python/ensembl/io/genomio/utils/json_utils.py
src/python/ensembl_genomio.egg-info/PKG-INFO
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src/python/tests/annotation/test_update_description.py
src/python/tests/annotation/test_update_description/gene1_desc.json
src/python/tests/annotation/test_update_description/gene1_nodesc.json
src/python/tests/annotation/test_update_description/gene1_syn.json
src/python/tests/annotation/test_update_description/gene1_syn_nouse.json
src/python/tests/annotation/test_update_description/gene1_xref.json
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src/python/tests/genbank/test_download.py
src/python/tests/genbank/test_extract_data.py
src/python/tests/genbank/test_extract_data_seq.py
src/python/tests/genbank/test_extract_data/input_file.gb
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src/python/tests/genome_metadata/test_extend.py
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src/python/tests/genome_metadata/test_prepare/genome_accession_ncbi.json
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src/python/tests/genome_metadata/test_prepare/updated_genome.json
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src/python/tests/genome_stats/test_compare.py
src/python/tests/genome_stats/test_dump.py
src/python/tests/genome_stats/test_compare/core_annotated.json
src/python/tests/genome_stats/test_compare/core_unannotated.json
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src/python/tests/genome_stats/test_compare/output_unannotated.json
src/python/tests/genome_stats/test_dump/genome_stats.json
src/python/tests/gff3/test_extract_annotation.py
src/python/tests/gff3/test_gene_merger.py
src/python/tests/gff3/test_id_allocator.py
src/python/tests/gff3/test_records.py
src/python/tests/gff3/test_restructure.py
src/python/tests/gff3/test_simplifier.py
src/python/tests/gff3/test_extract_annotation/dump_description.json
src/python/tests/gff3/test_extract_annotation/dump_noinfo.json
src/python/tests/gff3/test_extract_annotation/dump_syn.json
src/python/tests/gff3/test_gene_merger/merge_fasta_in.gff3
src/python/tests/gff3/test_gene_merger/merge_fasta_out.gff3
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src/python/tests/gff3/test_gene_merger/merge_unordered_in.gff3
src/python/tests/gff3/test_gene_merger/merge_unordered_out.gff3
src/python/tests/gff3/test_id_allocator/geneid_GeneID.gff3
src/python/tests/gff3/test_id_allocator/geneid_GeneID2.gff3
src/python/tests/gff3/test_id_allocator/geneid_bad.gff3
src/python/tests/gff3/test_id_allocator/geneid_makeid.gff3
src/python/tests/gff3/test_id_allocator/geneid_noGeneID.gff3
src/python/tests/gff3/test_id_allocator/geneid_ok.gff3
src/python/tests/gff3/test_id_allocator/pseudo_01.gff3
src/python/tests/gff3/test_id_allocator/pseudo_02_in.gff3
src/python/tests/gff3/test_id_allocator/pseudo_02_out.gff3
src/python/tests/gff3/test_id_allocator/pseudo_03_in.gff3
src/python/tests/gff3/test_id_allocator/pseudo_03_out.gff3
src/python/tests/gff3/test_id_allocator/pseudo_04.gff3
src/python/tests/gff3/test_records/invalid.gff
src/python/tests/gff3/test_records/record_n1.gff
src/python/tests/gff3/test_records/record_n2.gff
src/python/tests/gff3/test_simplifier/bad_gene_type.gff
src/python/tests/gff3/test_simplifier/bad_gene_type_skipped.gff
src/python/tests/gff3/test_simplifier/bad_subtr_type.gff
src/python/tests/gff3/test_simplifier/bad_tr_type.gff
src/python/tests/gff3/test_simplifier/gene_ignored.gff
src/python/tests/gff3/test_simplifier/gene_unsupported.gff
src/python/tests/gff3/test_simplifier/genes_badnames.gff
src/python/tests/gff3/test_simplifier/genes_badnames_brc4name.gff
src/python/tests/gff3/test_simplifier/genes_badnames_noname.gff
src/python/tests/gff3/test_simplifier/genome_brc4.json
src/python/tests/gff3/test_simplifier/genome_no_brc4.json
src/python/tests/gff3/test_simplifier/mobile_te.gff
src/python/tests/gff3/test_simplifier/ok_gene.gff
src/python/tests/gff3/test_simplifier/ok_protein_coding_gene.gff
src/python/tests/gff3/test_simplifier/ok_tr_ignored.gff
src/python/tests/gff3/test_simplifier/pseudogene.gff
src/python/tests/gff3/test_simplifier/pseudogene_cds.gff
src/python/tests/gff3/test_simplifier/pseudogene_cds_removed.gff
src/python/tests/gff3/test_simplifier/clean/extra.gff
src/python/tests/gff3/test_simplifier/clean/extra_clean.gff
src/python/tests/gff3/test_simplifier/lone/cds.gff
src/python/tests/gff3/test_simplifier/lone/cds_pseudo.gff
src/python/tests/gff3/test_simplifier/lone/cds_pseudo_simped.gff
src/python/tests/gff3/test_simplifier/lone/cds_simped.gff
src/python/tests/gff3/test_simplifier/lone/mrna.gff
src/python/tests/gff3/test_simplifier/lone/mrna_pseudo.gff
src/python/tests/gff3/test_simplifier/lone/mrna_pseudo_simped.gff
src/python/tests/gff3/test_simplifier/lone/mrna_simped.gff
src/python/tests/gff3/test_simplifier/lone/rrna.gff
src/python/tests/gff3/test_simplifier/lone/rrna_simped.gff
src/python/tests/gff3/test_simplifier/lone/transcript.gff
src/python/tests/gff3/test_simplifier/lone/transcript_simped.gff
src/python/tests/gff3/test_simplifier/lone/trna.gff
src/python/tests/gff3/test_simplifier/lone/trna_simped.gff
src/python/tests/gff3/test_simplifier/mirna/gene.gff
src/python/tests/gff3/test_simplifier/mirna/gene_simped.gff
src/python/tests/gff3/test_simplifier/mirna/nogene.gff
src/python/tests/gff3/test_simplifier/mirna/nogene_simped.gff
src/python/tests/gff3/test_simplifier/mirna/pseudo_nogene.gff
src/python/tests/gff3/test_simplifier/mirna/pseudo_nogene_simped.gff
src/python/tests/gff3/test_simplifier/mirna/pseudogene.gff
src/python/tests/gff3/test_simplifier/mirna/pseudogene_simped.gff
src/python/tests/gff3/test_simplifier/mirna/two_primary.gff
src/python/tests/gff3/test_simplifier/mirna/unsupported_tr.gff
src/python/tests/gff3/test_simplifier/non_gene/mobile_1name.gff
src/python/tests/gff3/test_simplifier/non_gene/mobile_1name_simped.gff3
src/python/tests/gff3/test_simplifier/non_gene/mobile_full.gff
src/python/tests/gff3/test_simplifier/non_gene/mobile_full_simped.gff
src/python/tests/gff3/test_simplifier/non_gene/te.gff
src/python/tests/manifest/test_check_integrity.py
src/python/tests/manifest/test_manifest.py
src/python/tests/manifest/test_manifest_stats.py
src/python/tests/manifest/test_check_integrity/functional_annotation.json
src/python/tests/manifest/test_check_integrity/manifest.json
src/python/tests/manifest/test_check_integrity/seq_region.json
src/python/tests/manifest/test_manifest/duplicates/agp1.agp
src/python/tests/manifest/test_manifest/duplicates/agp2.agp
src/python/tests/manifest/test_manifest/duplicates/manifest.json
src/python/tests/manifest/test_manifest/full_data/functional_annotation.json
src/python/tests/manifest/test_manifest/full_data/manifest.json
src/python/tests/manifest/test_manifest/full_data/seq_region.json
src/python/tests/manifest/test_manifest/invalid_checksum/agp1.agp
src/python/tests/manifest/test_manifest/invalid_checksum/manifest.json
src/python/tests/manifest/test_manifest/missing_files/manifest.json
src/python/tests/manifest/test_manifest/missing_files/seq_region.json
src/python/tests/manifest/test_manifest_stats/full_data/agp1.agp
src/python/tests/manifest/test_manifest_stats/full_data/agp2.agp
src/python/tests/manifest/test_manifest_stats/full_data/functional_annotation.json
src/python/tests/manifest/test_manifest_stats/full_data/manifest.json
src/python/tests/manifest/test_manifest_stats/full_data/seq_region.json
src/python/tests/manifest/test_manifest_stats/get_gff3/ok_gene.gff
src/python/tests/manifest/test_manifest_stats/get_gff3/pseudogene_cds.gff
src/python/tests/manifest/test_manifest_stats/get_gff3/te_gene.gff
src/python/tests/manifest/test_manifest_stats/manifest_empty/manifest.json
src/python/tests/manifest/test_manifest_stats/seq_regions/manifest.json
src/python/tests/manifest/test_manifest_stats/seq_regions/seq_region.json
src/python/tests/schemas/test_json.py
src/python/tests/schemas/test_json/functional_annotation.json
src/python/tests/schemas/test_json/functional_annotation_schema.json
src/python/tests/schemas/test_json/manifest.json
src/python/tests/schemas/test_json/seq_region.json
src/python/tests/seq_region/test_collection.py
src/python/tests/seq_region/test_dump.py
src/python/tests/seq_region/test_gbff.py
src/python/tests/seq_region/test_prepare.py
src/python/tests/seq_region/test_report.py
src/python/tests/seq_region/test_collection/apicoplast.gb
src/python/tests/seq_region/test_collection/report.txt
src/python/tests/seq_region/test_gbff/apicoplast.gb
src/python/tests/seq_region/test_gbff/apicoplast_linear.gb
src/python/tests/seq_region/test_gbff/apicoplast_nocomment.gb
src/python/tests/seq_region/test_gbff/apicoplast_nofeatures.gb
src/python/tests/seq_region/test_gbff/apicoplast_nogene.gb
src/python/tests/seq_region/test_gbff/apicoplast_noprefix_location.gb
src/python/tests/seq_region/test_gbff/apicoplast_simple_comment.gb
src/python/tests/seq_region/test_gbff/apicoplast_unknown_location.gb
src/python/tests/seq_region/test_prepare/apicoplast.gb
src/python/tests/seq_region/test_prepare/genome.json
src/python/tests/seq_region/test_prepare/report.txt
src/python/tests/seq_region/test_prepare/out/no_gbff.json
src/python/tests/seq_region/test_prepare/out/removed.json
src/python/tests/seq_region/test_prepare/out/with_gbff.json
src/python/tests/seq_region/test_report/report.txt
src/python/tests/seq_region/test_report/report_noheader.txt