CAPELLINI
User guide
Installation
External dependencies
Reference FASTAs
Quick start
Terminal UI
Programmatic API
Pipeline overview
Stages
Configuration
Key parameters
Inputs
Outputs
Reference
API reference
Top-level
capellini.config
capellini.pipeline
Stages
capellini.stages.preflight
capellini.stages.dada2
capellini.stages.ncbi_mapping
capellini.stages.mmseqs2
capellini.stages.spacepharer
capellini.stages.procs
capellini.stages.network
Utilities
capellini.utils.io
capellini.utils.taxonomy
capellini.utils.transforms
capellini.utils.network_utils
About
Citation
CAPELLINI
Index
Index
A
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B
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C
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D
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E
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F
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G
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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V
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W
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_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() (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_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)
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)
download_if_missing() (in module capellini.utils.io)
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)
full_ncbi_taxonomy_url (capellini.config.CapelliniConfig attribute)
G
genes_reference_url (capellini.config.CapelliniConfig attribute)
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)
ncbi_accessory_path (capellini.config.CapelliniConfig attribute)
ncbi_taxdmp_url (capellini.config.CapelliniConfig attribute)
O
open_maybe_gzip() (in module capellini.utils.io)
orient_W_viruses_by_bacteria() (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)
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_ref_url (capellini.config.CapelliniConfig attribute)
silva_taxmap_path (capellini.config.CapelliniConfig attribute)
silva_taxmap_url (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)
T
tax_bac_for_smoothing (capellini.config.CapelliniConfig attribute)
tax_vir (capellini.config.CapelliniConfig attribute)
to_yaml() (capellini.config.CapelliniConfig method)
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)