├── CAMPER.hmm ├── CAMPER_DRAMKit ├── camper_dramkit.egg-info │ ├── PKG-INFO │ ├── SOURCES.txt │ ├── dependency_links.txt │ ├── entry_points.txt │ ├── requires.txt │ └── top_level.txt ├── camper_dramkit │ ├── __init__.py │ ├── camper_annotate.py │ ├── camper_distill.py │ ├── combine_annotations_lowmem.py │ └── data │ │ └── CAMPER_blast.faa ├── dist │ └── camper_dramkit-1.0.13.tar.gz ├── environment.yaml ├── setup.py └── tests │ ├── test_camper_annotate.py │ ├── test_camper_distill.py │ └── test_data │ ├── CAZyDB.07312019.fam-activities.subset.txt │ ├── NC_001422.faa │ ├── NC_001422.fasta │ ├── NC_001422.mmsdb_h │ ├── Pfam-A_subset.full.gz │ ├── Pfam-A_subset.hmm.dat.gz │ ├── VIRSorter_affi-contigs.tab │ ├── annotated_fake_gff.gff │ ├── camper_test_annotations.tsv │ ├── camper_test_annotations_one.tsv │ ├── camper_test_distillate.tsv │ ├── camper_test_genes.faa │ ├── camper_test_genes_empty.faa │ ├── e_coli_16S.fasta │ ├── fake_gene_ko.link │ ├── fake_gff.gff │ ├── fake_trnas.tsv │ ├── hmm_thresholds.txt │ ├── hmmsearch_hit.txt │ ├── query_target_hits.b6 │ ├── target_query_hits.b6 │ ├── test_CONFIG │ ├── test_camper_blast_search_formater_hits.tsv │ ├── test_camper_blast_search_formater_out.csv │ ├── test_camper_blast_search_formater_scores.tsv │ ├── test_camper_hmmscan_formater_hits.csv │ ├── test_camper_hmmscan_formater_out.csv │ ├── test_camper_hmmscan_formater_out_notop_hit.csv │ ├── test_camper_hmmscan_formater_scores.tsv │ ├── trnas.fa │ ├── unformatted_cazy.b6 │ ├── unformatted_kofam.b6 │ ├── unformatted_vogdb.b6 │ └── vog_annotations_latest.subset.tsv.gz ├── CAMPER_RoadMap_v1.pdf ├── CAMPER_blast.faa ├── CAMPER_blast_scores.tsv ├── CAMPER_distillate.tsv ├── CAMPER_hmm_scores.tsv ├── CITATION.cff ├── LICENSE ├── README.md ├── compound_key.txt ├── figs ├── README.md └── camper_map.png └── raw_data └── building_HMMs ├── CHI ├── CHI_for_hmm_deduplicated_aligned.fasta ├── README.md ├── chi.mafftauto.gappyout.faa ├── chi.mafftauto.gappyout.faa.treefile ├── chi_uniref90_top300_exp.faa └── experimental_seeds.faa ├── DDR_TDR ├── README.md ├── ddr_for_hmm_deduplicated_aligned.fasta ├── ddr_tdr.mafftauto.faa ├── ddr_tdr.mafftauto.gappyout.faa ├── ddr_tdr.mafftauto.gappyout.faa.treefile ├── ddr_tdr_uniref90_top300_exp.faa ├── experimental_seeds.faa └── tdr_for_hmm_deduplicated_aligned.fasta ├── FCR_DZR ├── README.md ├── dzr_for_hmm_deduplicated_aligned.fasta ├── experimental_dzr.faa ├── experimental_fcr.faa ├── fcr.dzr.out_.mafftauto.gappyout.faa ├── fcr.dzr.out_.mafftauto.gappyout.faa.treefile ├── fcr_dzr_outgroup_uniref90_top100_pulled.faa └── fcr_for_hmm_deduplicated_aligned.fasta ├── FLR ├── README.md ├── experimental_seeds.faa ├── flr.mafftauto.gappyout.faa ├── flr.mafftauto.gappyout.faa.treefile ├── flr_for_hmm_deduplicated_aligned.fasta └── flr_uniref90_top300_exp.faa ├── LSD ├── README.md ├── experimental_seeds.faa ├── lsd_rzo_for_hmm_deduplicated_aligned.fasta ├── lsd_rzo_uniref90.mafftauto.gappyout.faa ├── 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