├── .gitattributes ├── .gitignore ├── .readthedocs.yml ├── CHANGELOG.md ├── LICENSE.txt ├── README.md ├── asv.conf.json ├── benchmarks ├── __init__.py └── benchmarks.py ├── bitbucket-pipelines.yml ├── conda.recipe └── meta.yaml ├── docs ├── Makefile ├── _static │ └── __init__.py ├── make.bat └── source │ ├── annotation_collection_overview.png │ ├── annotation_collections.ipynb │ ├── annotation_data_structures.rst │ ├── conf.py │ ├── exporting_to_files.ipynb │ ├── file_parsing.md │ ├── index.rst │ ├── instantiating_objects.ipynb │ ├── location_operations.ipynb │ ├── object_model.rst │ ├── object_model_overview.png │ ├── paradigm.rst │ ├── parent_operations.ipynb │ ├── parsing_genbank.ipynb │ ├── parsing_gff3.ipynb │ ├── parsing_variants.ipynb │ ├── sequence_operations.ipynb │ └── vignettes.ipynb ├── inscripta └── biocantor │ ├── __init__.py │ ├── constants.py │ ├── exc.py │ ├── gene │ ├── __init__.py │ ├── biotype.py │ ├── cds.py │ ├── cds_frame.py │ ├── codon.py │ ├── collections.py │ ├── feature.py │ ├── gene.py │ ├── interval.py │ ├── transcript.py │ └── variants.py │ ├── io │ ├── __init__.py │ ├── bed │ │ ├── __init__.py │ │ ├── bed.py │ │ └── exc.py │ ├── exc.py │ ├── fasta │ │ ├── __init__.py │ │ ├── exc.py │ │ └── fasta.py │ ├── features │ │ └── __init__.py │ ├── genbank │ │ ├── __init__.py │ │ ├── constants.py │ │ ├── exc.py │ │ ├── parser.py │ │ └── writer.py │ ├── gff3 │ │ ├── __init__.py │ │ ├── constants.py │ │ ├── exc.py │ │ ├── parser.py │ │ ├── rows.py │ │ └── writer.py │ ├── models.py │ ├── ncbi │ │ ├── __init__.py │ │ ├── exc.py │ │ └── tbl_writer.py │ ├── parser.py │ └── vcf │ │ ├── __init__.py │ │ └── parser.py │ ├── location │ ├── __init__.py │ ├── location.py │ ├── location_impl.py │ └── strand.py │ ├── parent │ ├── __init__.py │ └── parent.py │ ├── sequence │ ├── __init__.py │ ├── alphabet.py │ └── sequence.py │ └── util │ ├── __init__.py │ ├── bins.py │ ├── enum.py │ ├── hashing.py │ ├── object_validation.py │ ├── ordering.py │ └── types.py ├── pyproject.toml ├── setup.cfg ├── setup.py ├── tests ├── conftest.py ├── data │ ├── FRG2B.gff3 │ ├── FRG2B.json │ ├── INSC1003.example_variants.vcf │ ├── INSC1003.fa │ ├── INSC1003.gbk │ ├── INSC1003.gff3 │ ├── INSC1003.json │ ├── INSC1003_ambiguous_strand.gbk │ ├── INSC1003_duplicate_locus_tag.gb │ ├── INSC1003_embedded_extra_contig.fa │ ├── INSC1003_embedded_extra_contig.gff3 │ ├── INSC1003_embedded_extra_contig.tbl │ ├── INSC1003_embedded_extra_contig_duplicate.gff3 │ ├── INSC1003_extra_contig.fa │ ├── INSC1003_extra_contig_duplicate.fa │ ├── INSC1003_from_gbk.tbl │ ├── INSC1003_hybrid.gbk │ ├── INSC1003_misordered.gbk │ ├── INSC1003_missing_gene.gbk │ ├── INSC1003_no_genes.gbk │ ├── INSC1003_no_genes_misordered.gbk │ ├── INSC1003_tbl_edge_cases.gbk │ ├── INSC1003_tbl_edge_cases.tbl │ ├── INSC1003_test_multiple_transcripts.gbk │ ├── INSC1003_with_parent.json │ ├── INSC1003_wrong_missing_translation.gbk │ ├── INSC1006_chrI.fa │ ├── INSC1006_chrI.fa.fai │ ├── INSC1006_chrI.gbff │ ├── INSC1006_chrI.gff3 │ ├── INSC1006_chrI.json │ ├── INSC1006_chrI.simulated_variants.json │ ├── INSC1006_chrI.simulated_variants.vcf │ ├── INSC1006_chrI.tbl │ ├── INSC1006_chrI_CDS_outside_bounds.gb │ ├── INSC1006_chrI_duplicate.gbff │ ├── INSC1006_chrI_duplicate_gene_feature.gb │ ├── INSC1006_chrI_misordered.gb │ ├── INSC1006_chrI_mrna_before_gene.gb │ ├── INSC1006_chrI_with_features.gbff │ ├── INSC1006_wrong_feature_type.gbk │ ├── INSC1020_subset_gff3.gb │ ├── Inscripta_BL21.sqn │ ├── MG1655_subset.gbff │ ├── PEG10_minus1frameshift.gff3 │ ├── PEG10_minus1frameshift.json │ ├── PEG10_offset_gff3_fasta.fa │ ├── PEG10_offset_gff3_fasta.gff3 │ ├── PEG10_offset_gff3_fasta.tbl │ ├── R64_subset.gbff │ ├── SGCE.gff3 │ ├── SGCE.json │ ├── ToyChr_R64v5_overlapping_genes.gb │ ├── ToyChr_R64v5_overlapping_genes.json │ ├── broken_coordinates_1.gbk │ ├── broken_coordinates_2.gbk │ ├── caret_coordinates.gbk │ ├── collection_gff3_export_chromosome_coordinates.gff │ ├── collection_gff3_export_chunk_relative.gff │ ├── collection_gff3_export_subset_chromosome_coordinates.gff │ ├── feature_test_1.gff │ ├── feature_test_1.json │ ├── feature_test_2.gbk │ ├── feature_test_2.gff │ ├── feature_test_2.json │ ├── feature_test_2_gbk.json │ ├── feature_test_3.gbk │ ├── feature_test_locus_tag_error.gff │ ├── feature_test_non_gene_locus_tag.gff │ ├── gene_cds_direct_child.gff3 │ ├── gene_cds_direct_child.json │ ├── insO_frameshift.fa │ ├── insO_frameshift.gbk │ ├── insO_frameshift.gff3 │ ├── insO_frameshift.tbl │ ├── insO_frameshift_from_gbk.tbl │ ├── locus_tag_collision.gbk │ ├── multiple_cds_same_gene.gb │ ├── negative_strand_frame.gbk │ ├── overlapping_cds_feature.gb │ ├── positive_strand_frame.gbk │ ├── test_cds_only.gff │ ├── test_cds_only.json │ └── test_spliced.gbff ├── io │ ├── bed │ │ └── test_bed.py │ ├── fasta │ │ └── test_fasta_export.py │ ├── genbank │ │ ├── test_genbank_parser.py │ │ └── test_genbank_writer.py │ ├── gff3 │ │ ├── test_gff3_attributes.py │ │ ├── test_gff3_features.py │ │ ├── test_gff3_parser.py │ │ └── test_gff3_writer.py │ ├── tbl │ │ └── test_tbl_export.py │ ├── test_feature.py │ ├── test_frameshift.py │ ├── test_models.py │ ├── test_parser.py │ └── variants │ │ └── test_vcf_parser.py └── minimal │ ├── gene │ ├── test_biotype.py │ ├── test_cds.py │ ├── test_codon.py │ ├── test_collections.py │ ├── test_feature_interval.py │ ├── test_interval.py │ ├── test_transcript.py │ └── test_variants.py │ ├── location │ ├── test_compound_interval.py │ ├── test_empty_location.py │ ├── test_single_interval.py │ └── test_strand.py │ ├── parent │ └── test_parent.py │ ├── sequence │ └── test_sequence.py │ └── util │ ├── test_hashing.py │ └── test_object_validation.py └── tox.ini /.gitattributes: -------------------------------------------------------------------------------- 1 | inscripta/biocantor/_version.py export-subst 2 | -------------------------------------------------------------------------------- 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