Index

A

add_taxonomy (capellini.config.CapelliniConfig attribute) aggregate_otu_columns_by_rank_skip_nan() (in module capellini.utils.network_utils) aggregate_viral_rank (capellini.config.CapelliniConfig attribute)

align_abundance_from_metadata() (in module capellini.utils.network_utils) apply_custom_renames() (in module capellini.utils.taxonomy) assign_crispr() (in module capellini.utils.network_utils) assign_ncbi_taxids() (in module capellini.utils.taxonomy)

B

bacContigs_reference_url (capellini.config.CapelliniConfig attribute) bacteria_fasta_name (capellini.config.CapelliniConfig attribute) bacteria_otu (capellini.config.CapelliniConfig attribute) bacteria_taxonomy (capellini.config.CapelliniConfig attribute) BACTERIA_TAXONOMY_RANK (capellini.config.CapelliniConfig attribute) BACTERIAL_RANKS (capellini.config.CapelliniConfig attribute) bacterial_raw_fasta_folder (capellini.config.CapelliniConfig attribute) BACTERIAL_WEIGHTS (capellini.config.CapelliniConfig attribute) base (capellini.config.CapelliniConfig attribute) batch_size (capellini.config.CapelliniConfig attribute) build_binary_crispr_matrix() (in module capellini.utils.network_utils) build_common_abundance_one() (in module capellini.stages.network)

build_name_to_ncbi() (in module capellini.utils.taxonomy) build_pa_matrix() (in module capellini.stages.procs) build_rank_to_taxids() (in module capellini.utils.taxonomy) build_raw_crispr_one() (in module capellini.stages.network) build_shrinkage_one() (in module capellini.stages.network) build_smooth_crispr_one() (in module capellini.stages.network) build_smoothed_crispr_for_study() (in module capellini.utils.network_utils) build_taxonomy_kernel_from_shared_ranks() (in module capellini.utils.network_utils) build_top200_dicts() (in module capellini.stages.mmseqs2) build_xstar_from_smoothed_crispr() (in module capellini.utils.network_utils) build_xstar_from_smoothed_crispr_residual() (in module capellini.utils.network_utils) build_xstar_one() (in module capellini.stages.network)

C

capellini.config module capellini.pipeline module capellini.stages.dada2 module capellini.stages.mmseqs2 module capellini.stages.ncbi_mapping module capellini.stages.network module capellini.stages.preflight module capellini.stages.procs module capellini.stages.spacepharer module capellini.utils.io module

capellini.utils.network_utils module capellini.utils.taxonomy module capellini.utils.transforms module CapelliniConfig (class in capellini.config) CapelliniPipeline (class in capellini.pipeline) check_and_install_spacepharer() (in module capellini.stages.spacepharer) clean_bacteria_taxonomy() (in module capellini.utils.taxonomy) clean_df_ids() (in module capellini.utils.taxonomy) clean_index_ids() (in module capellini.utils.taxonomy) closure() (in module capellini.utils.transforms) clr() (in module capellini.utils.transforms) clustering_path (capellini.config.CapelliniConfig attribute) combine_protein_collections() (in module capellini.stages.procs) compute_spacepharer_stats() (in module capellini.stages.spacepharer) crispr_matrix_aggregate_viruses() (in module capellini.utils.network_utils) CRISPR_SMOOTH_ALPHA (capellini.config.CapelliniConfig attribute)

D

dada2_folder (capellini.config.CapelliniConfig attribute) default() (capellini.config.CapelliniConfig class method) direction (capellini.config.CapelliniConfig attribute)

double_clr_transform() (in module capellini.utils.transforms) download_ncbi_names() (in module capellini.stages.ncbi_mapping) download_path (capellini.config.CapelliniConfig attribute) download_protein_reference() (in module capellini.stages.procs)

E

enhanced_networks_folder (capellini.config.CapelliniConfig attribute) extend_taxonomy (capellini.config.CapelliniConfig attribute) extract_bacterial_proteins() (in module capellini.stages.procs)

extract_ids_from_header() (in module capellini.stages.mmseqs2) extract_ids_from_reference() (in module capellini.stages.mmseqs2) extract_spacers() (capellini.stages.spacepharer.SpacePHARERWorkflow method) extract_viral_proteins() (in module capellini.stages.procs)

F

fallback_pick_from_space() (in module capellini.stages.mmseqs2) fasta_generation (capellini.config.CapelliniConfig attribute) fdr (capellini.config.CapelliniConfig attribute) filter_1bac_1vir (capellini.config.CapelliniConfig attribute)

filter_target_spacers() (in module capellini.stages.spacepharer) fresh_start (capellini.config.CapelliniConfig attribute) from_dict() (capellini.config.CapelliniConfig class method) from_yaml() (capellini.config.CapelliniConfig class method) full_ncbi_taxonomy_path (capellini.config.CapelliniConfig attribute)

G

genes_reference_url (capellini.config.CapelliniConfig attribute) geometric_mean_safe() (in module capellini.utils.transforms)

get_hierarchies() (in module capellini.utils.network_utils) get_reference_16s() (in module capellini.stages.mmseqs2) get_spacers_collection() (in module capellini.stages.spacepharer)

I

input_fasta_folder (capellini.config.CapelliniConfig attribute)

is_16s_gene() (in module capellini.stages.mmseqs2) isolate_ref_16S (capellini.config.CapelliniConfig attribute)

K

KEEP_COLUMN (capellini.config.CapelliniConfig attribute)

keep_coords (capellini.config.CapelliniConfig attribute) keep_spacers_collection (capellini.config.CapelliniConfig attribute)

L

LAM (capellini.config.CapelliniConfig attribute)

load_bacteria_taxonomy() (in module capellini.utils.taxonomy) lookup_ncbi_taxid() (in module capellini.utils.taxonomy)

M

make_db() (capellini.stages.spacepharer.SpacePHARERWorkflow method) map_silva_to_progenomes_bounded() (in module capellini.stages.mmseqs2) mapping_saving (capellini.config.CapelliniConfig attribute) matrix_type (capellini.config.CapelliniConfig attribute) max_length (capellini.config.CapelliniConfig attribute) max_matches (capellini.config.CapelliniConfig attribute) metadata_path (capellini.config.CapelliniConfig attribute) min_bitscore (capellini.config.CapelliniConfig attribute) min_length (capellini.config.CapelliniConfig attribute) min_n_spacers (capellini.config.CapelliniConfig attribute) mmseq_folder (capellini.config.CapelliniConfig attribute) module capellini.config capellini.pipeline capellini.stages.dada2 capellini.stages.mmseqs2 capellini.stages.ncbi_mapping capellini.stages.network capellini.stages.preflight capellini.stages.procs capellini.stages.spacepharer capellini.utils.io capellini.utils.network_utils capellini.utils.taxonomy capellini.utils.transforms

N

N_STEPS (capellini.config.CapelliniConfig attribute)

normalize_columns() (in module capellini.utils.transforms)

O

old_style_clr_transform() (in module capellini.utils.transforms) open_maybe_gzip() (in module capellini.utils.io) orient_W_viruses_by_bacteria() (in module capellini.utils.network_utils)

out_path() (in module capellini.utils.network_utils) OUTPUT_ROOT (capellini.config.CapelliniConfig attribute) OVERWRITE (capellini.config.CapelliniConfig attribute)

P

parse_bool_series() (in module capellini.utils.taxonomy) parse_mmseqs_output() (in module capellini.stages.mmseqs2) phage_host_predictions (capellini.config.CapelliniConfig attribute) pick_bounded() (in module capellini.stages.mmseqs2) plot_spacepharer_figures() (in module capellini.stages.spacepharer) predict() (capellini.stages.spacepharer.SpacePHARERWorkflow method) prepare_bacteria_genus_abundance() (in module capellini.utils.network_utils)

PRESERVE_SCALE (capellini.config.CapelliniConfig attribute) PREVALENCE (capellini.config.CapelliniConfig attribute) prevalence_filter_df() (in module capellini.utils.network_utils) procs_folder (capellini.config.CapelliniConfig attribute) protein_reference_url (capellini.config.CapelliniConfig attribute) proteins_extraction_path (capellini.config.CapelliniConfig attribute) PSEUDOCOUNT (capellini.config.CapelliniConfig attribute)

Q

quick_stats() (capellini.stages.spacepharer.SpacePHARERWorkflow method)

R

read_table() (in module capellini.utils.io) ref_removal (capellini.config.CapelliniConfig attribute) regenerate_16S_reference (capellini.config.CapelliniConfig attribute) regenerate_spacers_collection (capellini.config.CapelliniConfig attribute) remove_collections (capellini.config.CapelliniConfig attribute) remove_decomp_fasta (capellini.config.CapelliniConfig attribute) remove_disease_columns_from_virus_abundance() (in module capellini.utils.network_utils) rename_clostridium_sensu_stricto() (in module capellini.utils.taxonomy) residual_message_passing() (in module capellini.utils.network_utils) residual_message_passing_df() (in module capellini.utils.network_utils) row_normalize() (in module capellini.utils.transforms) run_all() (capellini.pipeline.CapelliniPipeline method) RUN_COMMON_ABUNDANCE (capellini.config.CapelliniConfig attribute) run_dada2() (in module capellini.stages.dada2)

run_from() (capellini.pipeline.CapelliniPipeline method) run_mmseqs2() (in module capellini.stages.mmseqs2) run_mmseqs_clustering() (in module capellini.stages.procs) run_mmseqs_easy_search() (in module capellini.stages.mmseqs2) run_ncbi_mapping() (in module capellini.stages.ncbi_mapping) run_network() (in module capellini.stages.network) run_preflight() (in module capellini.stages.preflight) run_procs() (in module capellini.stages.procs) RUN_RAW_CRISPR_NETWORKS (capellini.config.CapelliniConfig attribute) RUN_SHRINKAGE_CORRELATIONS (capellini.config.CapelliniConfig attribute) RUN_SMOOTH_CRISPR (capellini.config.CapelliniConfig attribute) run_spacepharer() (in module capellini.stages.spacepharer) run_stage() (capellini.pipeline.CapelliniPipeline method) RUN_XSTAR (capellini.config.CapelliniConfig attribute)

S

sanitize_index() (in module capellini.utils.taxonomy) sanitize_taxon_name() (in module capellini.utils.taxonomy) save_single_bacgenome_collection (capellini.config.CapelliniConfig attribute) schaefer_strimmer_corr() (in module capellini.utils.transforms) sh() (in module capellini.utils.io) silva_ref_path (capellini.config.CapelliniConfig attribute) silva_taxmap_path (capellini.config.CapelliniConfig attribute) smooth_crispr_bac_vir() (in module capellini.utils.network_utils)

sp_folder (capellini.config.CapelliniConfig attribute) SpacePHARERWorkflow (class in capellini.stages.spacepharer) species_level (capellini.config.CapelliniConfig attribute) STAGE_LABELS (capellini.pipeline.CapelliniPipeline attribute) STAGE_ORDER (capellini.pipeline.CapelliniPipeline attribute) STUDY (capellini.config.CapelliniConfig attribute) study_outdir() (in module capellini.utils.network_utils) summarize_df() (in module capellini.utils.network_utils)

T

tax_bac_for_smoothing (capellini.config.CapelliniConfig attribute) tax_vir (capellini.config.CapelliniConfig attribute) to_yaml() (capellini.config.CapelliniConfig method)

transform_message_passing_smoothed_crispr() (in module capellini.utils.network_utils) transform_message_passing_smoothed_crispr_df() (in module capellini.utils.network_utils) TRANSPOSE_RAW_CRISPR_AFTER_LOAD (capellini.config.CapelliniConfig attribute)

V

VERBOSE (capellini.config.CapelliniConfig attribute) viral_ranks (capellini.config.CapelliniConfig attribute) viral_weights (capellini.config.CapelliniConfig attribute)

virus_abundance_raw (capellini.config.CapelliniConfig attribute) virus_fasta_name (capellini.config.CapelliniConfig attribute) virus_fasta_path() (capellini.config.CapelliniConfig method)

W

write_df() (in module capellini.utils.io)