Index

A

add_samples() (assnake.api.sample_set.SampleSet method) assnake (module) assnake.api (module) assnake.api.bb_stats (module) assnake.api.dada2 (module) assnake.api.dataset (module) assnake.api.fs_helpers (module) assnake.api.init_config (module) assnake.api.loaders (module) assnake.api.mg_py (module) assnake.api.new_loaders (module) assnake.api.prep (module)

assnake.api.sample_set (module) assnake.api.snake_module (module) assnake.api.update_fs_samples (module) assnake.cli (module) assnake.cli.assnake_cli (module) assnake.cli.commands (module) assnake.cli.commands.cmd_run (module) assnake.cli.commands.commands_assembly (module) assnake.cli.commands.dataset_commands (module) assnake.cli.commands.download_data_command (module) assnake.cli.commands.init (module) assnake.cli.import_samples_to_df (module) assnake.utils (module)

B

basic_info() (in module assnake.api.bb_stats)

biospecimens (assnake.api.dataset.Dataset attribute) bytes2human() (in module assnake.utils)

C

check_if_assnake_is_initialized() (in module assnake.utils) config (assnake.api.sample_set.SampleSet attribute)

create_links() (in module assnake.api.fs_helpers) create_taxa_count_from_dada2() (in module assnake.api.mg_py)

D

Dataset (class in assnake.api.dataset) delete_ds() (in module assnake.api.fs_helpers) df (assnake.api.dataset.Dataset attribute)

df_full_info() (in module assnake.api.loaders) dict_norm_print() (in module assnake.utils) download_from_url() (in module assnake.utils)

F

fill_and_write_config() (in module assnake.api.init_config) filter_mp2() (in module assnake.api.loaders) find_files() (in module assnake.api.fs_helpers) (in module assnake.cli.import_samples_to_df)

fs_prefix (assnake.api.dataset.Dataset attribute) full_path (assnake.api.dataset.Dataset attribute)

G

general_taxa() (assnake.api.sample_set.SampleSet method) general_taxa_one() (in module assnake.api.loaders) get_config_loc() (in module assnake.utils) get_cov_stats() (in module assnake.api.bb_stats) get_df_from_query() (in module assnake.api.bb_stats) get_full_track() (in module assnake.api.dada2) get_general_taxa_comp_krak_style() (in module assnake.api.loaders)

get_internal_config() (in module assnake.utils) get_locs_for_result() (assnake.api.sample_set.SampleSet method) get_sample_dict_from_dir() (in module assnake.api.fs_helpers) (in module assnake.cli.import_samples_to_df) get_samples_from_dir() (in module assnake.api.fs_helpers) (in module assnake.cli.import_samples_to_df) get_url_remote_file_size() (in module assnake.utils) graph_of_calls() (in module assnake.utils)

H

human2bytes() (in module assnake.utils)

I

initialization_commands (assnake.api.snake_module.SnakeModule attribute)

install_dir (assnake.api.snake_module.SnakeModule attribute) invocation_commands (assnake.api.snake_module.SnakeModule attribute)

L

load_biospecimens_in_df() (in module assnake.api.loaders) load_centrifuge() (in module assnake.api.bb_stats) load_config_file() (in module assnake.utils) load_count() (in module assnake.api.loaders) load_cov_stats() (in module assnake.api.bb_stats) load_coverage() (in module assnake.api.bb_stats) load_df_from_db() (in module assnake.api.loaders) load_dfs_from_db() (in module assnake.api.loaders) load_hm2() (in module assnake.api.loaders) load_hm2_grouped() (in module assnake.api.loaders)

load_mag_contigs() (in module assnake.api.loaders) load_mags_info() (in module assnake.api.loaders) load_mg_samples_in_df() (in module assnake.api.loaders) load_mg_samples_in_df_fs() (in module assnake.api.loaders) load_mp2_new() (in module assnake.api.loaders) load_mp2_old() (in module assnake.api.loaders) load_resanal_reports() (in module assnake.api.loaders) load_sample() (in module assnake.api.loaders) load_samples_metadata() (in module assnake.api.loaders) load_sources_in_df() (in module assnake.api.loaders) load_wc_config() (in module assnake.utils)

M

main() (in module assnake.cli.assnake_cli) (in module assnake.cli.import_samples_to_df)

mg_samples (assnake.api.dataset.Dataset attribute) mg_samples_for_df_fs() (in module assnake.api.loaders)

N

name (assnake.api.snake_module.SnakeModule attribute)

P

pathizer() (in module assnake.utils) plot_coverage() (in module assnake.api.bb_stats) plot_gc_cov_portrait() (in module assnake.api.bb_stats) plot_gc_cov_portrait_mult() (in module assnake.api.bb_stats) plot_portrait_with_diff() (in module assnake.api.bb_stats) prepare() (in module assnake.api.bb_stats)

prepare_assembly_set() (assnake.api.sample_set.SampleSet method) prepare_dada2_sample_list() (assnake.api.sample_set.SampleSet method) prepare_list_for_multiqc_fastqc() (in module assnake.api.prep) prepare_mothur_set() (assnake.api.sample_set.SampleSet method) prepare_samples_for_dada2() (in module assnake.api.prep) print_seq() (in module assnake.api.bb_stats)

R

read_krak_node() (in module assnake.api.loaders) read_yaml() (in module assnake.utils) reads_info (assnake.api.sample_set.SampleSet attribute)

remove_outliers() (in module assnake.api.bb_stats) rename_seqs_to_asvs() (in module assnake.api.dada2) roller() (in module assnake.api.bb_stats)

S

sample_sets (assnake.api.dataset.Dataset attribute) samples_in_df() (in module assnake.api.loaders) samples_pd (assnake.api.sample_set.SampleSet attribute), [1] samples_to_pd() (in module assnake.api.loaders) SampleSet (class in assnake.api.sample_set)

show_av_dict() (in module assnake.cli.commands.dataset_commands) single_level_from_mp2_table() (in module assnake.api.mg_py) snakefiles (assnake.api.snake_module.SnakeModule attribute) SnakeModule (class in assnake.api.snake_module) sources (assnake.api.dataset.Dataset attribute)

T

tax_glom() (in module assnake.api.mg_py)

to_dict() (assnake.api.dataset.Dataset method) to_nucl_res() (in module assnake.api.bb_stats)

U

update_config() (in module assnake.utils)

update_fs_samples_csv() (in module assnake.api.update_fs_samples)

W

wc_config (assnake.api.sample_set.SampleSet attribute)

wc_configs (assnake.api.snake_module.SnakeModule attribute)