├── .DS_Store ├── .gitattributes ├── .gitignore ├── BioSAK.egg-info ├── PKG-INFO ├── SOURCES.txt ├── dependency_links.txt ├── requires.txt └── top_level.txt ├── BioSAK ├── .DS_Store ├── .RData ├── .Rhistory ├── BLCA_op_parser.py ├── BioSAK_config.py ├── COG2020.py ├── COG2024.py ├── COG_boxplot_last1row.R ├── COG_boxplot_last2row.R ├── CheckM.py ├── Combine_KEGG_COG.py ├── Combine_KEGG_arCOG.py ├── DendroDF.py ├── DendroDF │ ├── Rscript_pheatmap_tree_subset_33_Nitrosopumilaceae_Matrix_distance.R │ ├── tree_subset_33_Nitrosopumilaceae_Matrix_distance.txt │ ├── tree_subset_33_Nitrosopumilaceae_Matrix_distance_Heatmap_BC_BC.pdf │ ├── tree_subset_33_Nitrosopumilaceae_Matrix_distance_Heatmap_BC_BC.txt │ ├── tree_subset_33_Nitrosopumilaceae_Matrix_distance_Heatmap_Eu_Eu.pdf │ └── tree_subset_33_Nitrosopumilaceae_Matrix_distance_Heatmap_Eu_Eu.txt ├── DnaFeaturesViewer.py ├── FastaSplitler_by_num.py ├── FastaSplitler_by_size.py ├── FasterqDump.py ├── GTDB_for_BLCA.py ├── GenBank.py ├── Gene2Ctg.py ├── KEGG.py ├── KEGG_boxplot_last1row.R ├── KEGG_get_eukaryotic_kos.py ├── KeepRemovingTmp.py ├── MeanMappingDepth.py ├── MetaBiosample.py ├── MetaCHIP_phylo.hmm ├── MetaCyc_reactions_with_ec.txt ├── NetEnzymes.py ├── Prodigal.py ├── Reads_simulator.py ├── RunGraphMB.py ├── SILVA_for_BLCA.py ├── SankeyTaxon.py ├── SubsampleLongReads.py ├── Tax4Fun2IndOTU.py ├── UNITE_for_BLCA.py ├── Usearch16S.py ├── VERSION ├── VisBlastOp.py ├── VisGeneFlk.py ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-310.pyc │ ├── __init__.cpython-35.pyc │ ├── __init__.cpython-37.pyc │ ├── global_functions.cpython-310.pyc │ └── global_functions.cpython-37.pyc ├── abd.backup.py ├── abd.py ├── abd_16s_amplicon.py ├── abd_16s_metagenome.py ├── abd_mask.py ├── abd_rename_and_combine.py ├── abund.py ├── add_desc.py ├── arCOG.py ├── bam2reads.py ├── blast.py ├── blca.py ├── blca_generate_abundance_table.py ├── blca_main.py ├── blca_subset_db_acc.py ├── blca_subset_db_gg.py ├── boxplot.py ├── boxplot_last1row.R ├── boxplot_matrix_COG.py ├── boxplot_matrix_COG_backup.py ├── boxplot_matrix_KEGG.py ├── boxplot_matrix_dbCAN.py ├── cat_fa.py ├── cdb.py ├── cdb_to_itol_piechart.py ├── cdd2cog.pl ├── checkm_marker.py ├── combine_fun_stats.py ├── combine_low_abd_otu.py ├── compare_sets.py ├── count_num.py ├── cross_link_seqs.py ├── dbCAN.py ├── download_GenBank_genome_subset_prokaryotes_csv.py ├── enrich.py ├── exe_cmds.py ├── ezaai2mat.py ├── fa2id.py ├── fastaai.py ├── format_converter.py ├── fq2fa.py ├── gapseq.py ├── gbk2faa.py ├── gbk2ffn.py ├── gbk2fna.py ├── gbk2gff.py ├── gbk_to_ffn_faa.py ├── gc.py ├── get_EC_from_ko_stats_D.py ├── get_GTDB_taxon_gnm.py ├── get_MAG_reads_long.py ├── get_Pfam_hmms.py ├── get_TopHits_taxonomy.py ├── get_aa_composition.py ├── get_abd1_mask.py ├── get_abd3_stats.py ├── get_bin_abundance copy.py ├── get_data_matrix.py ├── get_eu_otu.py ├── get_gene_depth.py ├── get_genome_GTDB.py ├── get_genome_NCBI.py ├── get_genome_NCBI_v1.py ├── get_genome_NCBI_v2.py ├── get_gnm_size.py ├── get_ko_gene_seqs.py ├── get_krona_plot.py ├── get_reads_from_sam.py ├── get_reads_id_in_sam.py ├── get_single_page_web.py ├── get_top_hit.py ├── get_total_length.py ├── gff2chrom.py ├── global_functions.py ├── hpc4.py ├── js_cmds.py ├── js_hpc3.py ├── keep_best_hit.py ├── ko00001.keg ├── koala.py ├── link_16S_MAG.py ├── link_16s.py ├── magabund.py ├── magabund2.py ├── manipulator_fasta.py ├── manipulator_msa.py ├── manipulator_newick.py ├── manipulator_sam.py ├── mann_whitney_u.py ├── mean_MAG_cov.py ├── merge_df.py ├── merge_seq.py ├── metaAssembly.py ├── metabat2concoct.py ├── metabat2maxbin.py ├── metadata.py ├── mmseqs.py ├── msa_to_distance_matrix.py ├── ncbi_dataset.py ├── odp.py ├── parse_MetaCyc_RxnDB.py ├── parse_mmseqs_tsv.py ├── plot_mag.py ├── plot_sam_depth.py ├── plot_tree.R ├── prefix_file.py ├── prefix_seq_by_file_name.py ├── prokka.py ├── reads2bam.py ├── rename_df_row.py ├── rename_reads_for_Reago.py ├── rename_seq.py ├── ribbon.py ├── rm_low_abd_otu.py ├── rm_low_depth_sample.py ├── sam2bam.py ├── sampling_GTDB_gnms.py ├── sankey.R ├── sankey.py ├── select_seq.py ├── sep_reads_by_barcode.py ├── slice_seq.py ├── split_fasta.py ├── split_folder.py ├── split_sam.py ├── sra.py ├── srun.py ├── statsTaxa.py ├── stats_arcog.py ├── stats_blast_hit.py ├── stats_cog2024.py ├── stats_ko.py ├── submitHPC.py ├── subset_GTDB_meta.py ├── subset_df.py ├── subset_tree.py ├── taxdump.py ├── tmp_1.py ├── tmp_2.py ├── tmp_3.py ├── tmp_4.py ├── tmp_5.py ├── top_16S_hits.py ├── top_hits_in_a_group.py ├── transpose.py ├── trim.py ├── usearch_uc.py ├── vis_color_scheme.py └── wilcox.py ├── BioSAK_tutorial ├── .DS_Store ├── Demo_batch_download_GenBank_genomes │ ├── Alteromonas.csv │ ├── Archaea.csv │ ├── Demo_batch_download_GenBank_genomes.png │ └── README.md ├── Demo_functional_annotation │ ├── .DS_Store │ ├── README.md │ ├── faa_files │ │ ├── NorthSea_bin014.faa │ │ ├── NorthSea_bin022.faa │ │ ├── NorthSea_bin028.faa │ │ ├── NorthSea_bin029.faa │ │ └── NorthSea_bin034.faa │ └── ffn_files │ │ ├── NorthSea_bin014.ffn │ │ ├── NorthSea_bin022.ffn │ │ ├── NorthSea_bin028.ffn │ │ ├── NorthSea_bin029.ffn │ │ └── NorthSea_bin034.ffn ├── Demo_single_page_web │ ├── README.md │ ├── doc │ │ ├── images │ │ │ ├── iNaturalist Blue Tube Sponge 2.jpg │ │ │ ├── iNaturalist Blue Tube Sponge 3.jpg │ │ │ ├── iNaturalist Blue Tube Sponge 4.jpg │ │ │ ├── iNaturalist Blue Tube Sponge.jpg │ │ │ ├── iNaturalist Chondrilla australiensis.jpg │ │ │ ├── iNaturalist Haliclona cymaeformis 2.jpeg │ │ │ ├── iNaturalist Haliclona cymaeformis 3.jpg │ │ │ ├── iNaturalist Haliclona cymaeformis 4.jpg │ │ │ ├── iNaturalist Haliclona cymaeformis.jpg │ │ │ ├── iNaturalist Heteropia glomerosa.jpeg │ │ │ ├── iNaturalist Mycale cecilia.jpg │ │ │ ├── iNaturalist Tethya robusta.jpg │ │ │ ├── iNaturalist Vagabond Boring Sponge 2.jpg │ │ │ ├── iNaturalist Vagabond Boring Sponge 3.jpeg │ │ │ ├── iNaturalist Vagabond Boring Sponge.jpg │ │ │ ├── iNaturalist_1.jpeg │ │ │ ├── iNaturalist_2.jpeg │ │ │ ├── iNaturalist_3.jpg │ │ │ ├── iNaturalist_4.jpg │ │ │ ├── iNaturalist_5.jpeg │ │ │ ├── iNaturalist_6.jpeg │ │ │ ├── iNaturalist_7.jpeg │ │ │ ├── iNaturalist_8.jpg │ │ │ └── iNaturalist_9.jpg │ │ ├── metadata.txt │ │ ├── template.html │ │ ├── template_with_barchart.html │ │ ├── webpage_with_barchart.png │ │ └── webpage_without_barchart.png │ ├── get_single_page_web.py │ ├── index.html │ ├── single_page_web.html │ └── single_page_web_with_barchart.html ├── Demo_tree_visualization_with_iTol │ ├── .DS_Store │ ├── README.md │ ├── figures │ │ ├── Layout_Circular.jpg │ │ ├── Layout_Normal copy.jpg │ │ ├── Layout_Normal.jpg │ │ ├── Step_1.jpg │ │ ├── Step_2.jpg │ │ ├── Tree_1.jpg │ │ ├── Tree_2.jpg │ │ └── Tree_with_functions_with_size.jpg │ └── files_needed │ │ ├── .DS_Store │ │ ├── abundance.txt │ │ ├── color_lifestyle.txt │ │ ├── color_taxon.txt │ │ ├── lifestyle.txt │ │ ├── size.txt │ │ ├── taxon.txt │ │ └── tree.newick ├── Tax4Fun2 │ ├── .DS_Store │ ├── README.md │ ├── Tax4Fun2_1.1.5.tar.gz │ ├── Tax4Fun2_example_cmds.R │ ├── demo_OTU.fasta │ ├── demo_OTU_table.csv │ └── demo_Tax4Fun2_outputs.zip └── example_files │ └── js_cmds │ ├── cmds_gapseq.txt │ └── js_header.txt ├── LICENSE ├── MANIFEST.in ├── README.md ├── bin ├── BioSAK └── __init__.py ├── demo_data ├── .DS_Store ├── enrich │ ├── annotation_files │ │ ├── .DS_Store │ │ ├── APA_bin_1.txt │ │ ├── APA_bin_3.txt │ │ ├── APA_bin_4.txt │ │ ├── COS36386_bin_1.txt │ │ ├── COS36386_bin_2.txt │ │ ├── COS36386_bin_3.txt │ │ ├── COS4_bin_47.txt │ │ ├── COS4_bin_49.txt │ │ ├── COS4_bin_51.txt │ │ ├── COS4_bin_55.txt │ │ ├── IRC3_bin_18.txt │ │ ├── IRC3_bin_19.txt │ │ ├── IRC3_bin_20.txt │ │ ├── IRC3_bin_21.txt │ │ ├── IRC3_bin_22.txt │ │ ├── IRC3_bin_25.txt │ │ ├── IRC4_bin_10.txt │ │ ├── IRC4_bin_11.txt │ │ ├── IRC4_bin_49.txt │ │ ├── IRC4_bin_9.txt │ │ ├── IRC_PAM_SB0665_bin_10.txt │ │ ├── IRC_PAM_SB0665_bin_11.txt │ │ ├── IRC_PAM_SB0665_bin_5.txt │ │ ├── IRC_PAM_SB0665_bin_8.txt │ │ ├── IRC_PAM_SB0665_bin_9.txt │ │ ├── PER4_bin_1.txt │ │ ├── RHO1_bin_1.txt │ │ ├── RHO1_bin_2.txt │ │ ├── RHO1_bin_3.txt │ │ ├── RHO1_bin_4.txt │ │ ├── RHO1_bin_6.txt │ │ ├── RHO2_bin_30.txt │ │ ├── RHO2_bin_31.txt │ │ ├── RHO2_bin_33.txt │ │ ├── RHO2_bin_35.txt │ │ ├── RHO3_bin_10.txt │ │ ├── RHO3_bin_11.txt │ │ ├── RHO3_bin_43.txt │ │ ├── RHO3_bin_9.txt │ │ ├── SPOO_karimiCosta_FZLQ01.txt │ │ ├── SPOO_karimiCosta_FZLR01.txt │ │ ├── SPOO_karimiCosta_FZLS01.txt │ │ ├── STY1_bin_1.txt │ │ ├── STY1_bin_2.txt │ │ ├── STY1_bin_3.txt │ │ ├── STY1_bin_5.txt │ │ ├── STY1_bin_6.txt │ │ ├── STY1_bin_7.txt │ │ ├── STY1_bin_8.txt │ │ ├── STY2_bin_1.txt │ │ ├── seawater_22112_bin_1.txt │ │ ├── seawater_22112_bin_10.txt │ │ ├── seawater_22112_bin_12.txt │ │ ├── seawater_22112_bin_14.txt │ │ ├── seawater_22112_bin_15.txt │ │ ├── seawater_22112_bin_16.txt │ │ ├── seawater_22112_bin_17.txt │ │ ├── seawater_22112_bin_2.txt │ │ ├── seawater_22112_bin_3.txt │ │ ├── seawater_22112_bin_4.txt │ │ ├── seawater_22112_bin_5.txt │ │ ├── seawater_22112_bin_6.txt │ │ ├── seawater_22112_bin_7.txt │ │ ├── seawater_22112_bin_8.txt │ │ ├── seawater_22112_bin_9.txt │ │ ├── seawater_bettina_36326_bin_26.txt │ │ ├── seawater_bettina_36326_bin_6.txt │ │ ├── seawater_bettina_36326_bin_7.txt │ │ ├── seawater_bettina_36327_bin_15.txt │ │ ├── seawater_bettina_36327_bin_2.txt │ │ ├── seawater_bettina_36327_bin_3.txt │ │ ├── seawater_bettina_36327_bin_4.txt │ │ ├── seawater_bettina_36327_bin_6.txt │ │ ├── seawater_bettina_36327_bin_7.txt │ │ ├── seawater_bettina_36328_bin_2.txt │ │ ├── seawater_seasim_SB9156_S5_bin_14.txt │ │ ├── seawater_seasim_SB9156_S5_bin_8.txt │ │ ├── seawater_seasim_SB9158_S7_bin_9.txt │ │ ├── seawater_seasim_SB9160_S9_bin_11.txt │ │ └── seawater_seasim_SB9160_S9_bin_9.txt │ └── grouping.txt ├── iTOL │ ├── LifeStyle_color.txt │ ├── MAG_abundance.txt │ ├── MAG_abundance_iTOL.txt │ ├── MAG_lifestyle.txt │ ├── MAG_lifestyle_iTOL.txt │ ├── MAG_size.txt │ ├── MAG_size_iTOL.txt │ ├── MAG_taxon.txt │ ├── MAG_taxon_iTOL_Range.txt │ ├── figures │ │ ├── Layout_Circular.jpg │ │ ├── Layout_Normal copy.jpg │ │ ├── Layout_Normal.jpg │ │ ├── Step_1.jpg │ │ ├── Step_2.jpg │ │ ├── Tree_1.jpg │ │ ├── Tree_2.jpg │ │ └── Tree_with_functions_with_size.jpg │ ├── species_tree.newick │ └── taxon_color.txt ├── merge_df │ ├── .DS_Store │ ├── df_1.txt │ ├── df_2.txt │ └── merged_df.txt ├── ribbon │ ├── .DS_Store │ ├── chrom_order.txt │ ├── demo_files │ │ ├── hydra.chrom │ │ ├── hydra.fa │ │ ├── hydra.pep │ │ ├── urchin.chrom │ │ ├── urchin.fa │ │ └── urchin.pep │ └── demo_outputs │ │ ├── BCnS_LGs_urchin_xy_synteny.pdf │ │ └── synteny_coloredby_CLG_v1.0.pdf ├── sankey │ ├── .DS_Store │ ├── demo_sankey_sankey.html │ ├── demo_sankey_sankey.txt │ └── sankey_matrix.txt ├── subset_df │ ├── cols_to_keep.txt │ ├── demo_df.txt │ └── rows_to_keep.txt └── vis_color_scheme │ ├── Sponge_full_lineage_GTDB_format.txt │ ├── color_code_sponge.pdf │ └── color_code_sponge.txt ├── dist ├── biosak-1.123.10-py3-none-any.whl └── biosak-1.123.10.tar.gz ├── doc ├── .DS_Store ├── BLCA_op_parser.md ├── BLCA_op_parser_cn.md ├── BestHit.md ├── BestHit_cn.md ├── COG2020.md ├── COG2020_cn.md ├── CheckM.md ├── CheckM_cn.md ├── GTDB_for_BLCA.md ├── GTDB_for_BLCA_cn.md ├── Index.md ├── Index_cn.md ├── KEGG.md ├── KEGG_cn.md ├── MeanMappingDepth.md ├── MeanMappingDepth_cn.md ├── Plot_MAG.md ├── Plot_MAG_cn.md ├── Reads_simulator.md ├── Reads_simulator_cn.md ├── RunGraphMB.md ├── RunGraphMB_cn.md ├── SILVA_for_BLCA.md ├── SILVA_for_BLCA_cn.md ├── SubsampleLongReads.md ├── SubsampleLongReads_cn.md ├── Tax4Fun2IndOTU.md ├── Tax4Fun2IndOTU_cn.md ├── VisGeneFlk.md ├── VisGeneFlk_cn.md ├── arCOG.md ├── arCOG_cn.md ├── bam2reads.md ├── bam2reads_cn.md ├── cat_fa.md ├── cat_fa_cn.md ├── cross_link_seqs.md ├── cross_link_seqs_cn.md ├── dbCAN.md ├── dbCAN_cn.md ├── exe_cmds.md ├── exe_cmds_cn.md ├── fa2id.md ├── fa2id_cn.md ├── ffn2faa.md ├── ffn2faa_cn.md ├── fq2fa.md ├── fq2fa_cn.md ├── full_list_modules.md ├── full_list_modules_cn.md ├── gbk2faa.md ├── gbk2faa_cn.md ├── gbk2ffn.md ├── gbk2ffn_cn.md ├── gbk2fna.md ├── gbk2fna_cn.md ├── get_GTDB_taxon_gnm.md ├── get_GTDB_taxon_gnm_cn.md ├── get_MAG_reads_long.md ├── get_MAG_reads_long_cn.md ├── get_Pfam_hmms.md ├── get_Pfam_hmms_cn.md ├── get_gene_depth.md ├── get_gene_depth_cn.md ├── get_genome_GTDB.md ├── get_genome_GTDB_cn.md ├── get_genome_NCBI.md ├── get_genome_NCBI_cn.md ├── get_gnm_size.md ├── get_gnm_size_cn.md ├── get_rc.md ├── get_rc_cn.md ├── gfa2fa.md ├── gfa2fa_cn.md ├── iTOL.md ├── iTOL_cn.md ├── js_cmds.md ├── js_cmds_cn.md ├── katana.md ├── katana_cn.md ├── magabund.md ├── magabund_cn.md ├── mean_MAG_cov.md ├── mean_MAG_cov_cn.md ├── merge_seq.md ├── merge_seq_cn.md ├── pdf │ └── Workflow_10_steps_to_design_a_bacterial_culture_medium.pdf ├── plot_sam_depth.md ├── plot_sam_depth_cn.md ├── reads2bam.md ├── reads2bam_cn.md ├── rename_reads_Reago.md ├── rename_reads_Reago_cn.md 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