LICENSE
README.md
pyproject.toml
mgnify_pipelines_toolkit/__init__.py
mgnify_pipelines_toolkit.egg-info/PKG-INFO
mgnify_pipelines_toolkit.egg-info/SOURCES.txt
mgnify_pipelines_toolkit.egg-info/dependency_links.txt
mgnify_pipelines_toolkit.egg-info/entry_points.txt
mgnify_pipelines_toolkit.egg-info/requires.txt
mgnify_pipelines_toolkit.egg-info/top_level.txt
mgnify_pipelines_toolkit/analysis/__init__.py
mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py
mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py
mgnify_pipelines_toolkit/analysis/amplicon/mapseq_to_asv_table.py
mgnify_pipelines_toolkit/analysis/amplicon/permute_primers.py
mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py
mgnify_pipelines_toolkit/analysis/amplicon/remove_ambiguous_reads.py
mgnify_pipelines_toolkit/analysis/amplicon/rev_comp_se_primers.py
mgnify_pipelines_toolkit/analysis/amplicon/study_summary_generator.py
mgnify_pipelines_toolkit/analysis/assembly/add_rhea_chebi_annotation.py
mgnify_pipelines_toolkit/analysis/assembly/antismash_gff_builder.py
mgnify_pipelines_toolkit/analysis/assembly/combined_gene_caller_merge.py
mgnify_pipelines_toolkit/analysis/assembly/generate_gaf.py
mgnify_pipelines_toolkit/analysis/assembly/gff_annotation_utils.py
mgnify_pipelines_toolkit/analysis/assembly/gff_file_utils.py
mgnify_pipelines_toolkit/analysis/assembly/gff_toolkit.py
mgnify_pipelines_toolkit/analysis/assembly/go_utils.py
mgnify_pipelines_toolkit/analysis/assembly/krona_txt_from_cat_classification.py
mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_cazys.py
mgnify_pipelines_toolkit/analysis/assembly/process_dbcan_result_clusters.py
mgnify_pipelines_toolkit/analysis/assembly/study_summary_generator.py
mgnify_pipelines_toolkit/analysis/assembly/summarise_antismash_bgcs.py
mgnify_pipelines_toolkit/analysis/assembly/summarise_goslims.py
mgnify_pipelines_toolkit/analysis/assembly/summarise_sanntis_bgcs.py
mgnify_pipelines_toolkit/analysis/genomes/__init__.py
mgnify_pipelines_toolkit/analysis/rawreads/study_summary_generator.py
mgnify_pipelines_toolkit/analysis/shared/__init__.py
mgnify_pipelines_toolkit/analysis/shared/amrintegrator.py
mgnify_pipelines_toolkit/analysis/shared/convert_cmscan_to_cmsearch_tblout.py
mgnify_pipelines_toolkit/analysis/shared/download_zenodo.py
mgnify_pipelines_toolkit/analysis/shared/dwc_summary_generator.py
mgnify_pipelines_toolkit/analysis/shared/fastq_suffix_header_check.py
mgnify_pipelines_toolkit/analysis/shared/gbk_generator.py
mgnify_pipelines_toolkit/analysis/shared/get_subunits.py
mgnify_pipelines_toolkit/analysis/shared/get_subunits_coords.py
mgnify_pipelines_toolkit/analysis/shared/library_strategy_check.py
mgnify_pipelines_toolkit/analysis/shared/mapseq2biom.py
mgnify_pipelines_toolkit/analysis/shared/markergene_study_summary.py
mgnify_pipelines_toolkit/analysis/shared/bgc/__init__.py
mgnify_pipelines_toolkit/analysis/shared/bgc/cli.py
mgnify_pipelines_toolkit/analysis/shared/bgc/gff_output.py
mgnify_pipelines_toolkit/analysis/shared/bgc/merge.py
mgnify_pipelines_toolkit/analysis/shared/bgc/models.py
mgnify_pipelines_toolkit/analysis/shared/bgc/sideload_json.py
mgnify_pipelines_toolkit/analysis/shared/bgc/tool_parsers.py
mgnify_pipelines_toolkit/analysis/shared/bgc/antismash_sideload_schemas/__init__.py
mgnify_pipelines_toolkit/analysis/shared/bgc/antismash_sideload_schemas/antismash_schema.py
mgnify_pipelines_toolkit/analysis/shared/bgc/antismash_sideload_schemas/build_models.py
mgnify_pipelines_toolkit/analysis/shared/gff/__init__.py
mgnify_pipelines_toolkit/analysis/shared/gff/io.py
mgnify_pipelines_toolkit/analysis/shared/proteins/__init__.py
mgnify_pipelines_toolkit/analysis/shared/proteins/parsers.py
mgnify_pipelines_toolkit/constants/db_labels.py
mgnify_pipelines_toolkit/constants/ncrna.py
mgnify_pipelines_toolkit/constants/regex_fasta_header.py
mgnify_pipelines_toolkit/constants/tax_ranks.py
mgnify_pipelines_toolkit/constants/thresholds.py
mgnify_pipelines_toolkit/constants/var_region_coordinates.py
mgnify_pipelines_toolkit/ena/__init__.py
mgnify_pipelines_toolkit/ena/create_reads_manifest.py
mgnify_pipelines_toolkit/ena/webin_cli_handler.py
mgnify_pipelines_toolkit/schemas/dataframes.py
mgnify_pipelines_toolkit/utils/__init__.py
mgnify_pipelines_toolkit/utils/fasta_to_delimited.py
mgnify_pipelines_toolkit/utils/get_mpt_version.py