LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
SchemaRefinery/__init__.py
SchemaRefinery/schema_refinery.py
SchemaRefinery.egg-info/PKG-INFO
SchemaRefinery.egg-info/SOURCES.txt
SchemaRefinery.egg-info/dependency_links.txt
SchemaRefinery.egg-info/entry_points.txt
SchemaRefinery.egg-info/requires.txt
SchemaRefinery.egg-info/top_level.txt
SchemaRefinery/AdaptLoci/AdaptLoci.py
SchemaRefinery/AdaptLoci/__init__.py
SchemaRefinery/AdaptLoci/Legacy_code/AdaptLoci.py
SchemaRefinery/CreateSchemaStructure/CreateSchemaStructure.py
SchemaRefinery/CreateSchemaStructure/__init__.py
SchemaRefinery/DownloadAssemblies/DownloadAssemblies.py
SchemaRefinery/DownloadAssemblies/__init__.py
SchemaRefinery/DownloadAssemblies/ena661k_assembly_fetcher.py
SchemaRefinery/DownloadAssemblies/fetch_metadata.py
SchemaRefinery/DownloadAssemblies/ncbi_datasets.py
SchemaRefinery/DownloadAssemblies/ncbi_linked_ids.py
SchemaRefinery/DownloadAssemblies/legacy_code/ncbi_assembly_fetcher_to_remove.py
SchemaRefinery/DownloadAssemblies/legacy_code/ncbi_linked_ids.py
SchemaRefinery/IdentifyParalogousLoci/IdentifyParalogousLoci.py
SchemaRefinery/IdentifyParalogousLoci/__init__.py
SchemaRefinery/MatchSchemas/MatchSchemas.py
SchemaRefinery/MatchSchemas/__init__.py
SchemaRefinery/RefineSchema/IdentifyDuplicateGenes.py
SchemaRefinery/RefineSchema/IdentifySpuriousGenes.py
SchemaRefinery/RefineSchema/__init__.py
SchemaRefinery/RefineSchema/Legacy_code/IdentifySpuriousGenes.py
SchemaRefinery/SchemaAnnotation/SchemaAnnotation.py
SchemaRefinery/SchemaAnnotation/__init__.py
SchemaRefinery/SchemaAnnotation/consolidate.py
SchemaRefinery/SchemaAnnotation/genbank_annotations.py
SchemaRefinery/SchemaAnnotation/proteome_fetcher.py
SchemaRefinery/SchemaAnnotation/proteome_matcher.py
SchemaRefinery/SchemaAnnotation/proteome_splitter.py
SchemaRefinery/SchemaAnnotation/legacy_code/genbank_annotations.py
SchemaRefinery/SchemaAnnotation/legacy_code/proteome_matcher.py
SchemaRefinery/docs/conf.py
SchemaRefinery/utils/Types.py
SchemaRefinery/utils/__init__.py
SchemaRefinery/utils/alignments_functions.py
SchemaRefinery/utils/blast_functions.py
SchemaRefinery/utils/classify_cds_functions.py
SchemaRefinery/utils/clustering_functions.py
SchemaRefinery/utils/constants.py
SchemaRefinery/utils/core_functions.py
SchemaRefinery/utils/decorators.py
SchemaRefinery/utils/download_functions.py
SchemaRefinery/utils/file_functions.py
SchemaRefinery/utils/globals.py
SchemaRefinery/utils/graphical_functions.py
SchemaRefinery/utils/iterable_functions.py
SchemaRefinery/utils/kmers_functions.py
SchemaRefinery/utils/linux_functions.py
SchemaRefinery/utils/logger_functions.py
SchemaRefinery/utils/pandas_functions.py
SchemaRefinery/utils/print_functions.py
SchemaRefinery/utils/sequence_functions.py
SchemaRefinery/utils/statistics.py
SchemaRefinery/utils/time_functions.py
SchemaRefinery/utils/validation.py
SchemaRefinery/utils/Legacy_code/core_functions.py
scripts/Extract_cgAlleles.py
scripts/N_split.py
scripts/alleles_frequency.py
scripts/assembly_statistics.py
scripts/cluster_distances.py
scripts/distance_matrix.py
scripts/distinct_variants.py
scripts/download_reads_ena.py
scripts/ena661k_assembly_fetcher.py
scripts/fetch_metadata.py
scripts/gc_content.py
scripts/inter_loci_validation.py
scripts/intra_loci_validation.py
scripts/loci_correspondence.py
scripts/loci_positions.py
scripts/locus_length_variability.py
scripts/locus_pairwise_graph.py
scripts/mask_matrix.py
scripts/match_schemas.py
scripts/merge_loci.py
scripts/missing_ids.py
scripts/ncbi_assembly_fetcher.py
scripts/ncbi_linked_ids.py
scripts/new_loci_annotations.py
scripts/paralogous_interloci_validation_merger.py
scripts/post_allelecall_plots.py
scripts/procompare.py
scripts/protein_diversity.py
scripts/reassign_ids.py
scripts/redundant_alleles.py
scripts/remove_loci.py
scripts/representative_susfinder.py
scripts/schema_validation_functions.py
scripts/split_locus.py
tests/__init__.py
tests/test_schema_refinery.py