├── .github └── workflows │ └── python-publish.yml ├── .gitignore ├── LICENSE ├── MetaBGC-Development ├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── docker │ ├── metabgc_docker_run │ └── run ├── job_scripts │ ├── runBLASTN.sbatch │ ├── runBLASTNArray.sh │ ├── runBuild.sh │ ├── runBuild_2.sh │ ├── runHMMER.sbatch │ ├── runHMMERArray.sh │ ├── runSearch.sh │ ├── runSearch_2.sh │ ├── synthesize_high.cmd │ └── synthesize_low.cmd ├── metabgc │ ├── __init__.py │ ├── metabgc_cmds.py │ ├── metadata │ │ ├── metahit_assembly_file.csv │ │ └── metahit_cohort.csv │ ├── src │ │ ├── EvaluateSpHMMs.R │ │ ├── __init__.py │ │ ├── addmetadatatofasta.py │ │ ├── blastrunlib.py │ │ ├── createsphmms.py │ │ ├── evaluate_sphmms.py │ │ ├── extractfastaseq.py │ │ ├── hmmerrunlib.py │ │ ├── hmmrecord.py │ │ ├── metabgcanalytics.py │ │ ├── metabgcbuild.py │ │ ├── metabgccluster.py │ │ ├── metabgcfindTP.py │ │ ├── metabgcidentify.py │ │ ├── metabgcquantify.py │ │ ├── metabgcsynthesize.py │ │ ├── producer_consumer.py │ │ ├── runBLASTN.sbatch │ │ ├── runBLASTNArray.sh │ │ ├── sphmmparser.py │ │ └── utils.py │ └── test │ │ ├── .gitignore │ │ ├── AbcK.zip │ │ ├── FosX │ │ ├── BinSampleCounts_Bodysite.tsv │ │ ├── BinSampleCounts_BodysiteAgg.tsv │ │ ├── BinSubjectCounts_Bodysite.tsv │ │ ├── BinSubjectCounts_BodysiteAgg.tsv │ │ ├── BodysiteBinVisitsAbundances.tsv │ │ ├── MaxBinSample.tsv │ │ ├── ReadLevelAbundance.tsv │ │ ├── ReadLevelBinStats.tsv │ │ ├── SampleAbundanceBodysite.tsv │ │ ├── SampleAbundanceBodysite_Stacked.tsv │ │ ├── SampleAbundanceMatrix.tsv │ │ ├── SubjectBinVisitCombined.tsv │ │ ├── Top10BinSample.tsv │ │ ├── bin_paths.txt │ │ ├── identified-quantified-biosynthetic-reads-blast.txt │ │ ├── identified_quantified_reads.fasta │ │ ├── identify_result │ │ │ └── spHMM-filtered-results.txt │ │ └── max_sample_assemblies.txt │ │ ├── OxyN.zip │ │ ├── analytics_test.py │ │ ├── build_test.py │ │ ├── cluster_test.py │ │ ├── identify_test.py │ │ └── quantify_test.py ├── partial_scripts │ ├── RLAP.py │ ├── RenameFastq.py │ ├── combine_RALP.py │ ├── download_ncbi.py │ ├── list.txt │ ├── misc_cmds.txt │ ├── nucmer_bin_assign.py │ ├── parse_HMM-results.py │ ├── quantifaction_gather.py │ └── update-HMM-fasta-headers.py ├── plot_scripts │ ├── SampleBinAbund_Heatmap.R │ └── plot_binning_results.py ├── pypi_build_cmds.txt ├── requirements.txt ├── runmetabgc.py └── setup.py ├── MetaBGC-V1.1 ├── LICENSE ├── MetaBGC-V1.1_Scripts │ ├── MetaBGC-Build │ │ ├── CreateSpHMMs.py │ │ ├── EmptyTemplate.yaml │ │ ├── EvaluateSpHMMs.R │ │ ├── GenSpHMMs.py │ │ ├── LanbioticsConfig.yaml │ │ ├── MetaBGC-Build.py │ │ ├── OxyNConfig.yaml │ │ ├── SPHMM_Model.Rmd │ │ ├── SiderophoresConfig.yaml │ │ ├── TcmIConfig.yaml │ │ ├── TcmJConfig.yaml │ │ ├── TcmNConfig.yaml │ │ └── runBuild.sh │ ├── MetaBGC-Cluster │ │ └── MetaBGC-Cluster.py │ ├── MetaBGC-Identify │ │ ├── ExtractFASTASeq.py │ │ ├── MetaBGC-Identify.py │ │ ├── __init__.py │ │ └── spHMM_parser.py │ ├── MetaBGC-Quantify │ │ ├── MetaBGC-Quantify.py │ │ └── add_metadata_to_FASTA.py │ └── Utils │ │ ├── HMMRecord.py │ │ └── Utils.py └── README.md ├── MetaBGC-V1 ├── LICENSE ├── MetaBGC-Build_Outputs │ ├── Cyclase_OxyN │ │ ├── Cyclase_OxyN_F1_cutoff.txt │ │ ├── Cyclase_OxyN__30_10__0_30.hmm │ │ ├── Cyclase_OxyN__30_10__130_160.hmm │ │ ├── Cyclase_OxyN__30_10__160_190.hmm │ │ ├── Cyclase_OxyN__30_10__170_200.hmm │ │ ├── Cyclase_OxyN__30_10__180_210.hmm │ │ ├── Cyclase_OxyN__30_10__190_220.hmm │ │ ├── Cyclase_OxyN__30_10__200_230.hmm │ │ ├── Cyclase_OxyN__30_10__210_240.hmm │ │ ├── Cyclase_OxyN__30_10__220_250.hmm │ │ ├── Cyclase_OxyN__30_10__240_270.hmm │ │ ├── Cyclase_OxyN__30_10__50_80.hmm │ │ ├── Cyclase_OxyN__30_10__60_90.hmm │ │ ├── Cyclase_OxyN__30_10__80_110.hmm │ │ ├── Cyclase_OxyN__30_10__90_120.hmm │ │ └── plot.eps │ ├── Cyclase_TcmI │ │ ├── Cyclase_TcmI_F1_Cutoff.txt │ │ ├── Cyclase_TcmI__30_10__0_30.hmm │ │ ├── Cyclase_TcmI__30_10__10_40.hmm │ │ ├── Cyclase_TcmI__30_10__20_50.hmm │ │ ├── Cyclase_TcmI__30_10__30_60.hmm │ │ ├── Cyclase_TcmI__30_10__40_70.hmm │ │ ├── Cyclase_TcmI__30_10__50_80.hmm │ │ ├── Cyclase_TcmI__30_10__60_90.hmm │ │ ├── Cyclase_TcmI__30_10__70_100.hmm │ │ ├── Cyclase_TcmI__30_10__80_110.hmm │ │ ├── Cyclase_TcmI__30_10__90_120.hmm │ │ └── plot.eps │ ├── Cyclase_TcmJ │ │ ├── Cyclase_TcmJ_F1_Cutoff.txt │ │ ├── Cyclase_TcmJ__30_10__0_30.hmm │ │ ├── Cyclase_TcmJ__30_10__10_40.hmm │ │ ├── Cyclase_TcmJ__30_10__20_50.hmm │ │ ├── Cyclase_TcmJ__30_10__30_60.hmm │ │ ├── Cyclase_TcmJ__30_10__40_70.hmm │ │ ├── Cyclase_TcmJ__30_10__90_120.hmm │ │ └── plot.eps │ ├── Cyclase_TcmN │ │ ├── Cyclase_TcmN_F1_Cutoff.txt │ │ ├── Cyclase_TcmN__30_10__150_180.hmm │ │ ├── Cyclase_TcmN__30_10__160_190.hmm │ │ ├── Cyclase_TcmN__30_10__170_200.hmm │ │ ├── Cyclase_TcmN__30_10__180_210.hmm │ │ ├── Cyclase_TcmN__30_10__210_240.hmm │ │ ├── Cyclase_TcmN__30_10__220_250.hmm │ │ ├── Cyclase_TcmN__30_10__230_260.hmm │ │ ├── Cyclase_TcmN__30_10__240_270.hmm │ │ ├── Cyclase_TcmN__30_10__250_280.hmm │ │ ├── Cyclase_TcmN__30_10__260_290.hmm │ │ └── plot.eps │ ├── IuA_IuC │ │ ├── IuA_IuC_F1_Cutoff.txt │ │ ├── IuA_IuC__30_10__0_30.hmm │ │ ├── IuA_IuC__30_10__10_40.hmm │ │ ├── IuA_IuC__30_10__20_50.hmm │ │ ├── IuA_IuC__30_10__240_270.hmm │ │ ├── IuA_IuC__30_10__250_280.hmm │ │ ├── IuA_IuC__30_10__260_290.hmm │ │ ├── IuA_IuC__30_10__300_330.hmm │ │ ├── IuA_IuC__30_10__30_60.hmm │ │ ├── IuA_IuC__30_10__320_350.hmm │ │ ├── IuA_IuC__30_10__330_360.hmm │ │ ├── IuA_IuC__30_10__340_370.hmm │ │ ├── IuA_IuC__30_10__350_380.hmm │ │ ├── IuA_IuC__30_10__360_390.hmm │ │ └── plot.eps │ └── LanC_like │ │ ├── LanC_like_F1_Cutoff.txt │ │ ├── LanC_like__30_10__200_230.hmm │ │ ├── LanC_like__30_10__280_310.hmm │ │ ├── LanC_like__30_10__330_360.hmm │ │ ├── LanC_like__30_10__340_370.hmm │ │ ├── LanC_like__30_10__350_380.hmm │ │ └── plot.eps ├── MetaBGC-V1_Benchmark_Data │ ├── Cyclase_OxyN │ │ ├── Cyclase_OxyN-True-Positive-genes.fasta │ │ ├── Cyclase_OxyN-full.hmm │ │ ├── Cyclase_OxyN.fasta │ │ ├── Gene_Interval_Pos.txt │ │ ├── segmented_alignments │ │ │ ├── Cyclase_OxyN__30_10__0_30.fas │ │ │ ├── Cyclase_OxyN__30_10__100_130.fas │ │ │ ├── Cyclase_OxyN__30_10__10_40.fas │ │ │ ├── Cyclase_OxyN__30_10__110_140.fas │ │ │ ├── Cyclase_OxyN__30_10__120_150.fas │ │ │ ├── Cyclase_OxyN__30_10__130_160.fas │ │ │ ├── Cyclase_OxyN__30_10__140_170.fas │ │ │ ├── Cyclase_OxyN__30_10__150_180.fas │ │ │ ├── Cyclase_OxyN__30_10__160_190.fas │ │ │ ├── Cyclase_OxyN__30_10__170_200.fas │ │ │ ├── Cyclase_OxyN__30_10__180_210.fas │ │ │ ├── Cyclase_OxyN__30_10__190_220.fas │ │ │ ├── Cyclase_OxyN__30_10__200_230.fas │ │ │ ├── Cyclase_OxyN__30_10__20_50.fas │ │ │ ├── Cyclase_OxyN__30_10__210_240.fas │ │ │ ├── Cyclase_OxyN__30_10__220_250.fas │ │ │ ├── Cyclase_OxyN__30_10__230_260.fas │ │ │ ├── Cyclase_OxyN__30_10__240_270.fas │ │ │ ├── Cyclase_OxyN__30_10__250_280.fas │ │ │ ├── Cyclase_OxyN__30_10__30_60.fas │ │ │ ├── Cyclase_OxyN__30_10__40_70.fas │ │ │ ├── Cyclase_OxyN__30_10__50_80.fas │ │ │ ├── Cyclase_OxyN__30_10__60_90.fas │ │ │ ├── Cyclase_OxyN__30_10__70_100.fas │ │ │ ├── Cyclase_OxyN__30_10__80_110.fas │ │ │ └── Cyclase_OxyN__30_10__90_120.fas │ │ └── spHMMs │ │ │ ├── Cyclase_OxyN__30_10__0_30.hmm │ │ │ ├── Cyclase_OxyN__30_10__100_130.hmm │ │ │ ├── Cyclase_OxyN__30_10__10_40.hmm │ │ │ ├── Cyclase_OxyN__30_10__110_140.hmm │ │ │ ├── Cyclase_OxyN__30_10__120_150.hmm │ │ │ ├── Cyclase_OxyN__30_10__130_160.hmm │ │ │ ├── Cyclase_OxyN__30_10__140_170.hmm │ │ │ ├── Cyclase_OxyN__30_10__150_180.hmm │ │ │ ├── Cyclase_OxyN__30_10__160_190.hmm │ │ │ ├── Cyclase_OxyN__30_10__170_200.hmm │ │ │ ├── Cyclase_OxyN__30_10__180_210.hmm │ │ │ ├── Cyclase_OxyN__30_10__190_220.hmm │ │ │ ├── Cyclase_OxyN__30_10__200_230.hmm │ │ │ ├── Cyclase_OxyN__30_10__20_50.hmm │ │ │ ├── Cyclase_OxyN__30_10__210_240.hmm │ │ │ ├── Cyclase_OxyN__30_10__220_250.hmm │ │ │ ├── Cyclase_OxyN__30_10__230_260.hmm │ │ │ ├── Cyclase_OxyN__30_10__240_270.hmm │ │ │ ├── Cyclase_OxyN__30_10__250_280.hmm │ │ │ ├── Cyclase_OxyN__30_10__30_60.hmm │ │ │ ├── Cyclase_OxyN__30_10__40_70.hmm │ │ │ ├── Cyclase_OxyN__30_10__50_80.hmm │ │ │ ├── Cyclase_OxyN__30_10__60_90.hmm │ │ │ ├── Cyclase_OxyN__30_10__70_100.hmm │ │ │ ├── Cyclase_OxyN__30_10__80_110.hmm │ │ │ └── Cyclase_OxyN__30_10__90_120.hmm │ ├── Cyclase_TcmI │ │ ├── Gene_Interval_Pos.txt │ │ ├── TcmI-True-Positive-genes.fasta │ │ ├── TcmI-full.hmm │ │ ├── TcmI.fasta │ │ ├── segmented_alignments │ │ │ ├── Cyclase_TcmI__30_10__0_30.fas │ │ │ ├── Cyclase_TcmI__30_10__10_40.fas │ │ │ ├── Cyclase_TcmI__30_10__20_50.fas │ │ │ ├── Cyclase_TcmI__30_10__30_60.fas │ │ │ ├── Cyclase_TcmI__30_10__40_70.fas │ │ │ ├── Cyclase_TcmI__30_10__50_80.fas │ │ │ ├── Cyclase_TcmI__30_10__60_90.fas │ │ │ ├── Cyclase_TcmI__30_10__70_100.fas │ │ │ ├── Cyclase_TcmI__30_10__80_110.fas │ │ │ └── Cyclase_TcmI__30_10__90_120.fas │ │ └── spHMMs │ │ │ ├── Cyclase_TcmI__30_10__0_30.hmm │ │ │ ├── Cyclase_TcmI__30_10__10_40.hmm │ │ │ ├── Cyclase_TcmI__30_10__20_50.hmm │ │ │ ├── Cyclase_TcmI__30_10__30_60.hmm │ │ │ ├── Cyclase_TcmI__30_10__40_70.hmm │ │ │ ├── Cyclase_TcmI__30_10__50_80.hmm │ │ │ ├── Cyclase_TcmI__30_10__60_90.hmm │ │ │ ├── Cyclase_TcmI__30_10__70_100.hmm │ │ │ ├── Cyclase_TcmI__30_10__80_110.hmm │ │ │ └── Cyclase_TcmI__30_10__90_120.hmm │ ├── Cyclase_TcmJ │ │ ├── Gene_Interval_Pos.txt │ │ ├── TcmJ-True-Positive-genes.fasta │ │ ├── TcmJ-full.hmm │ │ ├── TcmJ.fasta │ │ ├── segmented_alignments │ │ │ ├── Cyclase_TcmJ-v3__30_10__0_30.fas │ │ │ ├── Cyclase_TcmJ-v3__30_10__10_40.fas │ │ │ ├── Cyclase_TcmJ-v3__30_10__20_50.fas │ │ │ ├── Cyclase_TcmJ-v3__30_10__30_60.fas │ │ │ ├── Cyclase_TcmJ-v3__30_10__40_70.fas │ │ │ ├── Cyclase_TcmJ-v3__30_10__50_80.fas │ │ │ ├── Cyclase_TcmJ-v3__30_10__60_90.fas │ │ │ ├── Cyclase_TcmJ-v3__30_10__70_100.fas │ │ │ ├── Cyclase_TcmJ-v3__30_10__80_110.fas │ │ │ └── Cyclase_TcmJ-v3__30_10__90_120.fas │ │ └── spHMMs │ │ │ ├── Cyclase_TcmJ-v3__30_10__0_30.hmm │ │ │ ├── Cyclase_TcmJ-v3__30_10__10_40.hmm │ │ │ ├── Cyclase_TcmJ-v3__30_10__20_50.hmm │ │ │ ├── Cyclase_TcmJ-v3__30_10__30_60.hmm │ │ │ ├── Cyclase_TcmJ-v3__30_10__40_70.hmm │ │ │ ├── Cyclase_TcmJ-v3__30_10__50_80.hmm │ │ │ ├── Cyclase_TcmJ-v3__30_10__60_90.hmm │ │ │ ├── Cyclase_TcmJ-v3__30_10__70_100.hmm │ │ │ ├── Cyclase_TcmJ-v3__30_10__80_110.hmm │ │ │ └── Cyclase_TcmJ-v3__30_10__90_120.hmm │ ├── Cyclase_TcmN │ │ ├── Gene_Interval_Pos.txt │ │ ├── TcmN-True-Positive-genes.fasta │ │ ├── TcmN-full.hmm │ │ ├── TcmN.fasta │ │ ├── segmented_alignments │ │ │ ├── Cyclase_TcmN__30_10__150_180.fas │ │ │ ├── Cyclase_TcmN__30_10__160_190.fas │ │ │ ├── Cyclase_TcmN__30_10__170_200.fas │ │ │ ├── Cyclase_TcmN__30_10__180_210.fas │ │ │ ├── Cyclase_TcmN__30_10__190_220.fas │ │ │ ├── Cyclase_TcmN__30_10__200_230.fas │ │ │ ├── Cyclase_TcmN__30_10__210_240.fas │ │ │ ├── Cyclase_TcmN__30_10__220_250.fas │ │ │ ├── Cyclase_TcmN__30_10__230_260.fas │ │ │ ├── Cyclase_TcmN__30_10__240_270.fas │ │ │ ├── Cyclase_TcmN__30_10__250_280.fas │ │ │ ├── Cyclase_TcmN__30_10__260_290.fas │ │ │ ├── Cyclase_TcmN__30_10__270_300.fas │ │ │ ├── Cyclase_TcmN__30_10__280_310.fas │ │ │ ├── Cyclase_TcmN__30_10__290_320.fas │ │ │ ├── Cyclase_TcmN__30_10__300_330.fas │ │ │ └── Cyclase_TcmN__30_10__310_340.fas │ │ └── spHMMs │ │ │ ├── Cyclase_TcmN__30_10__150_180.hmm │ │ │ ├── Cyclase_TcmN__30_10__160_190.hmm │ │ │ ├── Cyclase_TcmN__30_10__170_200.hmm │ │ │ ├── Cyclase_TcmN__30_10__180_210.hmm │ │ │ ├── Cyclase_TcmN__30_10__190_220.hmm │ │ │ ├── Cyclase_TcmN__30_10__200_230.hmm │ │ │ ├── Cyclase_TcmN__30_10__210_240.hmm │ │ │ ├── Cyclase_TcmN__30_10__220_250.hmm │ │ │ ├── Cyclase_TcmN__30_10__230_260.hmm │ │ │ ├── Cyclase_TcmN__30_10__240_270.hmm │ │ │ ├── Cyclase_TcmN__30_10__250_280.hmm │ │ │ ├── Cyclase_TcmN__30_10__260_290.hmm │ │ │ ├── Cyclase_TcmN__30_10__270_300.hmm │ │ │ ├── Cyclase_TcmN__30_10__280_310.hmm │ │ │ ├── Cyclase_TcmN__30_10__290_320.hmm │ │ │ ├── Cyclase_TcmN__30_10__300_330.hmm │ │ │ └── Cyclase_TcmN__30_10__310_340.hmm │ ├── IuA_IuC │ │ ├── Gene_Interval_Pos.txt │ │ ├── IuA_IuC-True-Positive-genes.fasta │ │ ├── IuA_IuC-full.hmm │ │ ├── IuA_IuC.fasta │ │ ├── segmented_alignments │ │ │ ├── IuA_IuC__30_10__0_30.fas │ │ │ ├── IuA_IuC__30_10__100_130.fas │ │ │ ├── IuA_IuC__30_10__10_40.fas │ │ │ ├── IuA_IuC__30_10__110_140.fas │ │ │ ├── IuA_IuC__30_10__120_150.fas │ │ │ ├── IuA_IuC__30_10__130_160.fas │ │ │ ├── IuA_IuC__30_10__140_170.fas │ │ │ ├── IuA_IuC__30_10__150_180.fas │ │ │ ├── IuA_IuC__30_10__160_190.fas │ │ │ ├── IuA_IuC__30_10__170_200.fas │ │ │ ├── IuA_IuC__30_10__180_210.fas │ │ │ ├── IuA_IuC__30_10__190_220.fas │ │ │ ├── IuA_IuC__30_10__200_230.fas │ │ │ ├── IuA_IuC__30_10__20_50.fas │ │ │ ├── IuA_IuC__30_10__210_240.fas │ │ │ ├── IuA_IuC__30_10__220_250.fas │ │ │ ├── IuA_IuC__30_10__230_260.fas │ │ │ ├── IuA_IuC__30_10__240_270.fas │ │ │ ├── IuA_IuC__30_10__250_280.fas │ │ │ ├── IuA_IuC__30_10__260_290.fas │ │ │ ├── IuA_IuC__30_10__270_300.fas │ │ │ ├── IuA_IuC__30_10__280_310.fas │ │ │ ├── IuA_IuC__30_10__290_320.fas │ │ │ ├── IuA_IuC__30_10__300_330.fas │ │ │ ├── IuA_IuC__30_10__30_60.fas │ │ │ ├── IuA_IuC__30_10__310_340.fas │ │ │ ├── IuA_IuC__30_10__320_350.fas │ │ │ ├── IuA_IuC__30_10__330_360.fas │ │ │ ├── IuA_IuC__30_10__340_370.fas │ │ │ ├── IuA_IuC__30_10__350_380.fas │ │ │ ├── IuA_IuC__30_10__360_390.fas │ │ │ ├── IuA_IuC__30_10__370_400.fas │ │ │ ├── IuA_IuC__30_10__380_410.fas │ │ │ ├── IuA_IuC__30_10__390_420.fas │ │ │ ├── IuA_IuC__30_10__400_430.fas │ │ │ ├── IuA_IuC__30_10__40_70.fas │ │ │ ├── IuA_IuC__30_10__410_440.fas │ │ │ ├── IuA_IuC__30_10__420_450.fas │ │ │ ├── IuA_IuC__30_10__430_460.fas │ │ │ ├── IuA_IuC__30_10__440_470.fas │ │ │ ├── IuA_IuC__30_10__450_480.fas │ │ │ ├── IuA_IuC__30_10__50_80.fas │ │ │ ├── IuA_IuC__30_10__60_90.fas │ │ │ ├── IuA_IuC__30_10__70_100.fas │ │ │ ├── IuA_IuC__30_10__80_110.fas │ │ │ └── IuA_IuC__30_10__90_120.fas │ │ └── spHMMs │ │ │ ├── IuA_IuC__30_10__0_30.hmm │ │ │ ├── IuA_IuC__30_10__100_130.hmm │ │ │ ├── IuA_IuC__30_10__10_40.hmm │ │ │ ├── IuA_IuC__30_10__110_140.hmm │ │ │ ├── IuA_IuC__30_10__120_150.hmm │ │ │ ├── IuA_IuC__30_10__130_160.hmm │ │ │ ├── IuA_IuC__30_10__140_170.hmm │ │ │ ├── IuA_IuC__30_10__150_180.hmm │ │ │ ├── IuA_IuC__30_10__160_190.hmm │ │ │ ├── IuA_IuC__30_10__170_200.hmm │ │ │ ├── IuA_IuC__30_10__180_210.hmm │ │ │ ├── IuA_IuC__30_10__190_220.hmm │ │ │ ├── IuA_IuC__30_10__200_230.hmm │ │ │ ├── IuA_IuC__30_10__20_50.hmm │ │ │ ├── IuA_IuC__30_10__210_240.hmm │ │ │ ├── IuA_IuC__30_10__220_250.hmm │ │ │ ├── IuA_IuC__30_10__230_260.hmm │ │ │ ├── IuA_IuC__30_10__240_270.hmm │ │ │ ├── IuA_IuC__30_10__250_280.hmm │ │ │ ├── IuA_IuC__30_10__260_290.hmm │ │ │ ├── IuA_IuC__30_10__270_300.hmm │ │ │ ├── IuA_IuC__30_10__280_310.hmm │ │ │ ├── IuA_IuC__30_10__290_320.hmm │ │ │ ├── IuA_IuC__30_10__300_330.hmm │ │ │ ├── IuA_IuC__30_10__30_60.hmm │ │ │ ├── IuA_IuC__30_10__310_340.hmm │ │ │ ├── IuA_IuC__30_10__320_350.hmm │ │ │ ├── IuA_IuC__30_10__330_360.hmm │ │ │ ├── IuA_IuC__30_10__340_370.hmm │ │ │ ├── IuA_IuC__30_10__350_380.hmm │ │ │ ├── IuA_IuC__30_10__360_390.hmm │ │ │ ├── IuA_IuC__30_10__370_400.hmm │ │ │ ├── IuA_IuC__30_10__380_410.hmm │ │ │ ├── IuA_IuC__30_10__390_420.hmm │ │ │ ├── IuA_IuC__30_10__400_430.hmm │ │ │ ├── IuA_IuC__30_10__40_70.hmm │ │ │ ├── IuA_IuC__30_10__410_440.hmm │ │ │ ├── IuA_IuC__30_10__420_450.hmm │ │ │ ├── IuA_IuC__30_10__430_460.hmm │ │ │ ├── IuA_IuC__30_10__440_470.hmm │ │ │ ├── IuA_IuC__30_10__450_480.hmm │ │ │ ├── IuA_IuC__30_10__50_80.hmm │ │ │ ├── IuA_IuC__30_10__60_90.hmm │ │ │ ├── IuA_IuC__30_10__70_100.hmm │ │ │ ├── IuA_IuC__30_10__80_110.hmm │ │ │ └── IuA_IuC__30_10__90_120.hmm │ └── LanC_like │ │ ├── Gene_Interval_Pos.txt │ │ ├── LanC_like-True-Positive-genes.fasta │ │ ├── LanC_like-full.hmm │ │ ├── LanC_like.fasta │ │ ├── segmented_alignments │ │ ├── LanC_like__30_10__0_30.fas │ │ ├── LanC_like__30_10__100_130.fas │ │ ├── LanC_like__30_10__10_40.fas │ │ ├── LanC_like__30_10__110_140.fas │ │ ├── LanC_like__30_10__120_150.fas │ │ ├── LanC_like__30_10__130_160.fas │ │ ├── LanC_like__30_10__140_170.fas │ │ ├── LanC_like__30_10__150_180.fas │ │ ├── LanC_like__30_10__160_190.fas │ │ ├── LanC_like__30_10__170_200.fas │ │ ├── LanC_like__30_10__180_210.fas │ │ ├── LanC_like__30_10__190_220.fas │ │ ├── LanC_like__30_10__200_230.fas │ │ ├── LanC_like__30_10__20_50.fas │ │ ├── LanC_like__30_10__210_240.fas │ │ ├── LanC_like__30_10__220_250.fas │ │ ├── LanC_like__30_10__230_260.fas │ │ ├── LanC_like__30_10__240_270.fas │ │ ├── LanC_like__30_10__250_280.fas │ │ ├── LanC_like__30_10__260_290.fas │ │ ├── LanC_like__30_10__270_300.fas │ │ ├── LanC_like__30_10__280_310.fas │ │ ├── LanC_like__30_10__290_320.fas │ │ ├── LanC_like__30_10__300_330.fas │ │ ├── LanC_like__30_10__30_60.fas │ │ ├── LanC_like__30_10__310_340.fas │ │ ├── LanC_like__30_10__320_350.fas │ │ ├── LanC_like__30_10__330_360.fas │ │ ├── LanC_like__30_10__340_370.fas │ │ ├── LanC_like__30_10__350_380.fas │ │ ├── LanC_like__30_10__360_390.fas │ │ ├── LanC_like__30_10__370_400.fas │ │ ├── LanC_like__30_10__380_410.fas │ │ ├── LanC_like__30_10__390_420.fas │ │ ├── LanC_like__30_10__400_430.fas │ │ ├── LanC_like__30_10__40_70.fas │ │ ├── LanC_like__30_10__410_440.fas │ │ ├── LanC_like__30_10__420_450.fas │ │ ├── LanC_like__30_10__50_80.fas │ │ ├── LanC_like__30_10__60_90.fas │ │ ├── LanC_like__30_10__70_100.fas │ │ ├── LanC_like__30_10__80_110.fas │ │ └── LanC_like__30_10__90_120.fas │ │ └── spHMMs │ │ ├── LanC_like__30_10__0_30.hmm │ │ ├── LanC_like__30_10__100_130.hmm │ │ ├── LanC_like__30_10__10_40.hmm │ │ ├── LanC_like__30_10__110_140.hmm │ │ ├── LanC_like__30_10__120_150.hmm │ │ ├── LanC_like__30_10__130_160.hmm │ │ ├── LanC_like__30_10__140_170.hmm │ │ ├── LanC_like__30_10__150_180.hmm │ │ ├── LanC_like__30_10__160_190.hmm │ │ ├── LanC_like__30_10__170_200.hmm │ │ ├── LanC_like__30_10__180_210.hmm │ │ ├── LanC_like__30_10__190_220.hmm │ │ ├── LanC_like__30_10__200_230.hmm │ │ ├── LanC_like__30_10__20_50.hmm │ │ ├── LanC_like__30_10__210_240.hmm │ │ ├── LanC_like__30_10__220_250.hmm │ │ ├── LanC_like__30_10__230_260.hmm │ │ ├── LanC_like__30_10__240_270.hmm │ │ ├── LanC_like__30_10__250_280.hmm │ │ ├── LanC_like__30_10__260_290.hmm │ │ ├── LanC_like__30_10__270_300.hmm │ │ ├── LanC_like__30_10__280_310.hmm │ │ ├── LanC_like__30_10__290_320.hmm │ │ ├── LanC_like__30_10__300_330.hmm │ │ ├── LanC_like__30_10__30_60.hmm │ │ ├── LanC_like__30_10__310_340.hmm │ │ ├── LanC_like__30_10__320_350.hmm │ │ ├── LanC_like__30_10__330_360.hmm │ │ ├── LanC_like__30_10__340_370.hmm │ │ ├── LanC_like__30_10__350_380.hmm │ │ ├── LanC_like__30_10__360_390.hmm │ │ ├── LanC_like__30_10__370_400.hmm │ │ ├── LanC_like__30_10__380_410.hmm │ │ ├── LanC_like__30_10__390_420.hmm │ │ ├── LanC_like__30_10__400_430.hmm │ │ ├── LanC_like__30_10__40_70.hmm │ │ ├── LanC_like__30_10__410_440.hmm │ │ ├── LanC_like__30_10__420_450.hmm │ │ ├── LanC_like__30_10__50_80.hmm │ │ ├── LanC_like__30_10__60_90.hmm │ │ ├── LanC_like__30_10__70_100.hmm │ │ ├── LanC_like__30_10__80_110.hmm │ │ └── LanC_like__30_10__90_120.hmm ├── MetaBGC-V1_Scripts │ ├── MetaBGC-Build │ │ ├── CreateSpHMMs.py │ │ ├── EvaluateSpHMMs.R │ │ └── MetaBGC-Build.py │ ├── MetaBGC-Cluster │ │ └── MetaBGC-Cluster.py │ ├── MetaBGC-Identify │ │ ├── ExtractFASTASeq.py │ │ ├── MetaBGC-Identify.py │ │ └── spHMM_parser.py │ ├── MetaBGC-Quantify │ │ ├── MetaBGC-Quantify.py │ │ └── add_metadata_to_FASTA.py │ └── Utils │ │ ├── HMMRecord.py │ │ └── Utils.py └── README.md ├── Models ├── Cyclase_OxyN │ ├── Cyclase_OxyN_F1_Cutoff.tsv │ ├── Cyclase_OxyN__30_10__0_30.hmm │ ├── Cyclase_OxyN__30_10__130_160.hmm │ ├── Cyclase_OxyN__30_10__160_190.hmm │ ├── Cyclase_OxyN__30_10__170_200.hmm │ ├── Cyclase_OxyN__30_10__180_210.hmm │ ├── Cyclase_OxyN__30_10__190_220.hmm │ ├── Cyclase_OxyN__30_10__200_230.hmm │ ├── Cyclase_OxyN__30_10__210_240.hmm │ ├── Cyclase_OxyN__30_10__220_250.hmm │ ├── Cyclase_OxyN__30_10__60_90.hmm │ ├── Cyclase_OxyN__30_10__70_100.hmm │ ├── Cyclase_OxyN__30_10__80_110.hmm │ ├── Cyclase_OxyN__30_10__90_120.hmm │ └── plot.eps ├── Cyclase_TcmI │ ├── Cyclase_TcmI_F1_Cutoff.tsv │ ├── Cyclase_TcmI__30_10__0_30.hmm │ ├── Cyclase_TcmI__30_10__10_40.hmm │ ├── Cyclase_TcmI__30_10__20_50.hmm │ ├── Cyclase_TcmI__30_10__30_60.hmm │ ├── Cyclase_TcmI__30_10__40_70.hmm │ ├── Cyclase_TcmI__30_10__50_80.hmm │ ├── Cyclase_TcmI__30_10__60_90.hmm │ ├── Cyclase_TcmI__30_10__70_100.hmm │ ├── Cyclase_TcmI__30_10__80_110.hmm │ ├── Cyclase_TcmI__30_10__90_120.hmm │ └── plot.eps ├── Cyclase_TcmJ │ ├── Cyclase_TcmJ_F1_Cutoff.tsv │ ├── Cyclase_TcmJ__30_10__0_30.hmm │ ├── Cyclase_TcmJ__30_10__10_40.hmm │ ├── Cyclase_TcmJ__30_10__20_50.hmm │ ├── Cyclase_TcmJ__30_10__30_60.hmm │ ├── Cyclase_TcmJ__30_10__40_70.hmm │ ├── Cyclase_TcmJ__30_10__90_120.hmm │ └── plot.eps ├── Cyclase_TcmN │ ├── Cyclase_TcmN_F1_Cutoff.tsv │ ├── Cyclase_TcmN__30_10__150_180.hmm │ ├── Cyclase_TcmN__30_10__160_190.hmm │ ├── Cyclase_TcmN__30_10__170_200.hmm │ ├── Cyclase_TcmN__30_10__180_210.hmm │ ├── Cyclase_TcmN__30_10__210_240.hmm │ ├── Cyclase_TcmN__30_10__220_250.hmm │ ├── Cyclase_TcmN__30_10__230_260.hmm │ ├── Cyclase_TcmN__30_10__240_270.hmm │ ├── Cyclase_TcmN__30_10__250_280.hmm │ ├── Cyclase_TcmN__30_10__260_290.hmm │ └── plot.eps ├── IuA_IuC │ ├── IuA_IuC_F1_Cutoff.tsv │ ├── IuA_IuC__30_10__0_30.hmm │ ├── IuA_IuC__30_10__10_40.hmm │ ├── IuA_IuC__30_10__20_50.hmm │ ├── IuA_IuC__30_10__240_270.hmm │ ├── IuA_IuC__30_10__250_280.hmm │ ├── IuA_IuC__30_10__260_290.hmm │ ├── IuA_IuC__30_10__300_330.hmm │ ├── IuA_IuC__30_10__30_60.hmm │ ├── IuA_IuC__30_10__320_350.hmm │ ├── IuA_IuC__30_10__330_360.hmm │ ├── IuA_IuC__30_10__340_370.hmm │ ├── IuA_IuC__30_10__350_380.hmm │ ├── IuA_IuC__30_10__360_390.hmm │ └── plot.eps └── LanC_like │ ├── LanC_like_F1_Cutoff.tsv │ ├── LanC_like__30_10__200_230.hmm │ ├── LanC_like__30_10__280_310.hmm │ ├── LanC_like__30_10__330_360.hmm │ ├── LanC_like__30_10__340_370.hmm │ ├── LanC_like__30_10__350_380.hmm │ └── plot.eps ├── README.md └── docker-metabgc ├── Dockerfile └── build_cmds.txt /.github/workflows/python-publish.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/donia-lab/MetaBGC/HEAD/.github/workflows/python-publish.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/donia-lab/MetaBGC/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/donia-lab/MetaBGC/HEAD/LICENSE -------------------------------------------------------------------------------- /MetaBGC-Development/.gitignore: 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