Index

A

Abort abort() (click.Context method) add_argument() (click.OptionParser method) add_command() (click.Group method) add_option() (click.OptionParser method) add_source() (click.CommandCollection method) add_to_tree() (in module capalyzer.packet_builder.sub_factories.toxonomy_long_form) ags() (capalyzer.packet_parser.dataframes.DataTableFactory method) AGSFactory (class in capalyzer.packet_builder.sub_factories.ave_genome_size_factory) allow_extra_args (click.BaseCommand attribute) (click.Context attribute) allow_interspersed_args (click.BaseCommand attribute) (click.Context attribute) (click.OptionParser attribute)

alpha_diversity() (capalyzer.packet_parser.dataframes.DataTableFactory method) amr_alpha_diversity() (capalyzer.packet_parser.dataframes.DataTableFactory method) amr_beta_diversity() (capalyzer.packet_parser.dataframes.DataTableFactory method) amr_rarefaction() (capalyzer.packet_parser.dataframes.DataTableFactory method) AMRFactory (class in capalyzer.packet_builder.sub_factories.amr_factory) amrs() (capalyzer.packet_parser.dataframes.DataTableFactory method) ancestor_rank() (capalyzer.packet_parser.taxa_tree.NCBITaxaTree method) ancestors() (capalyzer.packet_parser.taxa_tree.NCBITaxaTree method) args (click.Context attribute) Argument (class in click) argument() (in module click) as_dist() (in module capalyzer.packet_builder.sub_factories.hmp_comparison_factory)

B

BadArgumentUsage BadOptionUsage BadParameter BaseCommand (class in click)

beta_diversity() (capalyzer.packet_parser.dataframes.DataTableFactory method) BOOL (in module click) bracken() (capalyzer.packet_builder.sub_factories.taxonomy_factory.TaxonomyFactory method) build_table() (in module capalyzer.packet_builder.sub_factories.toxonomy_long_form)

C

call_on_close() (click.Context method) callback (click.Command attribute) capalyzer (module) capalyzer.cli (module) capalyzer.constants (module) capalyzer.packet_builder (module) capalyzer.packet_builder.api (module) capalyzer.packet_builder.cli (module) capalyzer.packet_builder.sub_factories (module) capalyzer.packet_builder.sub_factories.amr_factory (module) capalyzer.packet_builder.sub_factories.ave_genome_size_factory (module) capalyzer.packet_builder.sub_factories.constants (module) capalyzer.packet_builder.sub_factories.hmp_comparison_factory (module) capalyzer.packet_builder.sub_factories.macrobes (module) capalyzer.packet_builder.sub_factories.microbe_directory (module) capalyzer.packet_builder.sub_factories.pathway_factory (module) capalyzer.packet_builder.sub_factories.read_proportions (module) capalyzer.packet_builder.sub_factories.subfactory (module) capalyzer.packet_builder.sub_factories.taxonomy_factory (module) capalyzer.packet_builder.sub_factories.toxonomy_long_form (module) capalyzer.packet_builder.sub_factories.utils (module) capalyzer.packet_builder.summary_table_factory (module) capalyzer.packet_builder.utils (module) capalyzer.packet_parser (module) capalyzer.packet_parser.cli (module) capalyzer.packet_parser.dataframes (module) capalyzer.packet_parser.diversity_metrics (module) capalyzer.packet_parser.longform_parser (module) capalyzer.packet_parser.taxa_tree (module) card_rpkm() (capalyzer.packet_builder.sub_factories.amr_factory.AMRFactory method)

card_rpkmg() (capalyzer.packet_builder.sub_factories.amr_factory.AMRFactory method) chao1() (in module capalyzer.packet_parser.diversity_metrics) Choice (class in click) classus() (capalyzer.packet_builder.sub_factories.amr_factory.AMRFactory method) clean_taxa() (in module capalyzer.packet_builder.sub_factories.taxonomy_factory) clear() (in module click) click (module) ClickException CliRunner (class in click.testing) close() (click.Context method) clr() (in module capalyzer.packet_parser.diversity_metrics) collect_usage_pieces() (click.Command method) (click.MultiCommand method) color (click.Context attribute) Command (class in click) command (click.Context attribute) command() (click.Group method) (in module click) command_path (click.Context attribute) CommandCollection (class in click) commands (click.Group attribute) confirm() (in module click) confirmation_option() (in module click) Context (class in click) context_settings (click.BaseCommand attribute) convert() (click.ParamType method) copy() (capalyzer.packet_parser.dataframes.DataTableFactory method) core_taxa() (capalyzer.packet_parser.dataframes.DataTableFactory method) csv_in_dir() (capalyzer.packet_parser.dataframes.DataTableFactory method) ctx (click.OptionParser attribute)

D

DataTableFactory (class in capalyzer.packet_parser.dataframes)

dedent() (click.HelpFormatter method) dists() (capalyzer.packet_builder.sub_factories.hmp_comparison_factory.HMPFactory method)

E

echo() (in module click) echo_via_pager() (in module click) edit() (in module click) ensure_object() (click.Context method)

envvar_list_splitter (click.ParamType attribute) exc_info (click.testing.Result attribute) exception (click.testing.Result attribute) exit() (click.Context method) exit_code (click.testing.Result attribute)

F

fail() (click.Context method) (click.ParamType method) File (class in click) FileError filter_dataframe() (capalyzer.packet_parser.dataframes.DataTableFactory method) find_object() (click.Context method) find_root() (click.Context method) FLOAT (in module click)

format_commands() (click.MultiCommand method) format_epilog() (click.Command method) format_filename() (in module click) format_help() (click.Command method) format_help_text() (click.Command method) format_options() (click.Command method) (click.MultiCommand method) format_usage() (click.Command method) forward() (click.Context method)

G

gene() (capalyzer.packet_builder.sub_factories.amr_factory.AMRFactory method) generic() (capalyzer.packet_builder.sub_factories.taxonomy_factory.TaxonomyFactory method) generic_card() (capalyzer.packet_builder.sub_factories.amr_factory.AMRFactory method) generic_megares() (capalyzer.packet_builder.sub_factories.amr_factory.AMRFactory method) genus() (capalyzer.packet_parser.taxa_tree.NCBITaxaTree method) get_ags_from_file() (in module capalyzer.packet_builder.sub_factories.ave_genome_size_factory) get_app_dir() (in module click) get_binary_stream() (in module click) get_command() (click.CommandCollection method) (click.Group method) (click.MultiCommand method) get_current_context() (in module click) get_default() (click.Parameter method) get_default_prog_name() (click.testing.CliRunner method) get_error_hint() (click.Parameter method) get_help() (click.Command method) (click.Context method) get_help_option() (click.Command method)

get_help_option_names() (click.Command method) get_metadata() (capalyzer.packet_builder.summary_table_factory.SummaryTableFactory method) get_metavar() (click.ParamType method) get_missing_message() (click.ParamType method) get_mpa_str() (in module capalyzer.packet_builder.sub_factories.toxonomy_long_form) get_node() (in module capalyzer.packet_builder.sub_factories.toxonomy_long_form) get_results() (capalyzer.packet_builder.summary_table_factory.SummaryTableFactory method) get_sample_name() (in module capalyzer.packet_builder.sub_factories.toxonomy_long_form) get_short_help_str() (click.Command method) get_terminal_size() (in module click) get_text_stream() (in module click) get_top_n() (in module capalyzer.packet_builder.sub_factories.taxonomy_factory) get_usage() (click.Context method) getchar() (in module click) getvalue() (click.HelpFormatter method) Group (class in click) group() (capalyzer.packet_builder.sub_factories.amr_factory.AMRFactory method) (click.Group method) (in module click)

H

help_option() (in module click) help_option_names (click.Context attribute) HelpFormatter (class in click)

hmp() (capalyzer.packet_parser.dataframes.DataTableFactory method) HMPFactory (class in capalyzer.packet_builder.sub_factories.hmp_comparison_factory) human_readable_name (click.Parameter attribute)

I

ignore_unknown_options (click.BaseCommand attribute) (click.Context attribute) (click.OptionParser attribute) indent() (click.HelpFormatter method) indentation() (click.HelpFormatter method) info_name (click.Context attribute) INT (in module click) IntRange (class in click) invoke() (click.BaseCommand method) (click.Command method) (click.Context method) (click.MultiCommand method) (click.testing.CliRunner method)

invoked_subcommand (click.Context attribute) is_rank() (in module capalyzer.packet_builder.sub_factories.taxonomy_factory) is_top_taxa() (in module capalyzer.packet_builder.sub_factories.taxonomy_factory) isolated_filesystem() (click.testing.CliRunner method) isolation() (click.testing.CliRunner method)

J

jensen_shannon_dist() (in module capalyzer.packet_parser.diversity_metrics) jloads() (in module capalyzer.packet_builder.sub_factories.hmp_comparison_factory) (in module capalyzer.packet_builder.sub_factories.macrobes) (in module capalyzer.packet_builder.sub_factories.microbe_directory) (in module capalyzer.packet_builder.sub_factories.read_proportions)

K

kraken() (capalyzer.packet_builder.sub_factories.taxonomy_factory.TaxonomyFactory method) krakenhll() (capalyzer.packet_builder.sub_factories.taxonomy_factory.TaxonomyFactory method)

krakenhll_angular() (capalyzer.packet_builder.sub_factories.taxonomy_factory.TaxonomyFactory method) krakenhll_long() (capalyzer.packet_builder.sub_factories.taxonomy_factory.TaxonomyFactory method)

L

launch() (in module click) list_commands() (click.CommandCollection method) (click.Group method) (click.MultiCommand method)

longform_taxa() (in module capalyzer.packet_builder.sub_factories.toxonomy_long_form) lookup_default() (click.Context method)

M

MacrobeFactory (class in capalyzer.packet_builder.sub_factories.macrobes) macrobes() (capalyzer.packet_parser.dataframes.DataTableFactory method) main() (click.BaseCommand method) make_all_tables() (in module capalyzer.packet_builder.api) make_context() (click.BaseCommand method) make_env() (click.testing.CliRunner method) make_formatter() (click.Context method) make_long_taxa() (in module capalyzer.packet_builder.api)

make_parser() (click.Command method) make_pass_decorator() (in module click) max_content_width (click.Context attribute) mech() (capalyzer.packet_builder.sub_factories.amr_factory.AMRFactory method) meta (click.Context attribute) metaphlan2() (capalyzer.packet_builder.sub_factories.taxonomy_factory.TaxonomyFactory method) MicrobeDirectoryFactory (class in capalyzer.packet_builder.sub_factories.microbe_directory) MultiCommand (class in click)

N

name (click.BaseCommand attribute) (click.ParamType attribute)

NCBITaxaTree (class in capalyzer.packet_parser.taxa_tree) NoSuchOption

O

obj (click.Context attribute) open_file() (in module click) Option (class in click)

option() (in module click) OptionParser (class in click) output (click.testing.Result attribute)

P

Parameter (class in click) params (click.Command attribute) (click.Context attribute) ParamType (class in click) parent (click.Context attribute) parent() (capalyzer.packet_parser.taxa_tree.NCBITaxaTree method) parse_args() (click.BaseCommand method) (click.Command method) (click.MultiCommand method) (click.OptionParser method) parse_files() (capalyzer.packet_parser.taxa_tree.NCBITaxaTree class method) parse_gene_table() (in module capalyzer.packet_builder.sub_factories.utils) parse_key_val_file() (in module capalyzer.packet_builder.utils) parse_krakenhll_report() (capalyzer.packet_builder.sub_factories.taxonomy_factory.TaxonomyFactory method)

parse_longform_taxa() (in module capalyzer.packet_parser.longform_parser) pass_context() (in module click) pass_obj() (in module click) password_option() (in module click) Path (class in click) PathwayFactory (class in capalyzer.packet_builder.sub_factories.pathway_factory) pathways() (capalyzer.packet_builder.sub_factories.pathway_factory.PathwayFactory method) (capalyzer.packet_parser.dataframes.DataTableFactory method) pause() (in module click) phyla() (capalyzer.packet_parser.taxa_tree.NCBITaxaTree method) process_value() (click.Parameter method) progressbar() (in module click) prompt() (in module click) protected_args (click.Context attribute)

R

random() (in module capalyzer.packet_parser.diversity_metrics) rank() (capalyzer.packet_parser.taxa_tree.NCBITaxaTree method) ranked_ancestors() (capalyzer.packet_parser.taxa_tree.NCBITaxaTree method) rarefaction() (capalyzer.packet_parser.dataframes.DataTableFactory method) rarefaction_analysis() (in module capalyzer.packet_parser.diversity_metrics) raw() (capalyzer.packet_builder.sub_factories.hmp_comparison_factory.HMPFactory method) (capalyzer.packet_builder.sub_factories.microbe_directory.MicrobeDirectoryFactory method) raw_table() (capalyzer.packet_builder.sub_factories.hmp_comparison_factory.HMPFactory method) (capalyzer.packet_builder.sub_factories.microbe_directory.MicrobeDirectoryFactory method) read_props() (capalyzer.packet_parser.dataframes.DataTableFactory method)

read_stats() (capalyzer.packet_parser.dataframes.DataTableFactory method) readJSON() (in module capalyzer.packet_builder.utils) ReadPropsFactory (class in capalyzer.packet_builder.sub_factories.read_proportions) report_from_tree() (in module capalyzer.packet_builder.sub_factories.toxonomy_long_form) resilient_parsing (click.Context attribute) Result (class in click.testing) result_callback (click.MultiCommand attribute) resultcallback() (click.MultiCommand method) rho_proportionality() (in module capalyzer.packet_parser.diversity_metrics) richness() (in module capalyzer.packet_parser.diversity_metrics) runner (click.testing.Result attribute)

S

scope() (click.Context method) secho() (in module click) section() (click.HelpFormatter method) set_metadata() (capalyzer.packet_parser.dataframes.DataTableFactory method) shannon_entropy() (in module capalyzer.packet_parser.diversity_metrics) single_rarefaction() (in module capalyzer.packet_parser.diversity_metrics) sources (click.CommandCollection attribute) split_envvar_value() (click.ParamType method)

stderr (click.testing.Result attribute) stderr_bytes (click.testing.Result attribute) stdout (click.testing.Result attribute) stdout_bytes (click.testing.Result attribute) STRING (in module click) style() (in module click) SubFactory (class in capalyzer.packet_builder.sub_factories.subfactory) SummaryTableFactory (class in capalyzer.packet_builder.summary_table_factory)

T

table() (capalyzer.packet_builder.sub_factories.macrobes.MacrobeFactory method) (capalyzer.packet_builder.sub_factories.read_proportions.ReadPropsFactory method) taxa_alpha_diversity() (capalyzer.packet_parser.dataframes.DataTableFactory method) taxa_beta_diversity() (capalyzer.packet_parser.dataframes.DataTableFactory method) taxa_rarefaction() (capalyzer.packet_parser.dataframes.DataTableFactory method) taxa_sort() (capalyzer.packet_parser.taxa_tree.NCBITaxaTree method) TaxaTree (class in capalyzer.packet_parser.taxa_tree) taxonomy() (capalyzer.packet_parser.dataframes.DataTableFactory method) TaxonomyFactory (class in capalyzer.packet_builder.sub_factories.taxonomy_factory)

tbl() (capalyzer.packet_builder.sub_factories.ave_genome_size_factory.AGSFactory method) terminal_width (click.Context attribute) tests (module) to_newick() (capalyzer.packet_parser.taxa_tree.TaxaTree method) token_normalize_func (click.Context attribute) tokenize() (in module capalyzer.packet_builder.sub_factories.toxonomy_long_form) (in module capalyzer.packet_builder.utils) Tuple (class in click) type_cast_value() (click.Parameter method)

U

UNPROCESSED (in module click) unstyle() (in module click)

UsageError UUID (in module click)

V

version_option() (in module click)

W

wrap_text() (in module click) write() (click.HelpFormatter method) write_csv() (in module capalyzer.packet_builder.api) write_dl() (click.HelpFormatter method)

write_heading() (click.HelpFormatter method) write_paragraph() (click.HelpFormatter method) write_text() (click.HelpFormatter method) write_usage() (click.HelpFormatter method)