Index

Symbols

16S

A

add_essentials() (BiomeAssembly method) align() (MultiSequenceAligner method)

annotate_nodes_by_map() (PhyloTree method) API

B

BiomeAssembly (class in pmaf.biome) BiomeSurvey (class in pmaf.biome) BranchestERABLE (class in pmaf.phylo.branchest) BranchestFastTree2 (class in pmaf.phylo.branchest) buckle_by_uid() (Nucleotide method) buckle_for_alignment() (MultiSequence method)

build() (TreeBuilderFastTree2 method) build_database_storage() (DatabaseGreengenes class method) (DatabaseGTDB class method) (DatabaseOTL class method) (DatabaseSILVA class method) (DatabaseUNITE class method)

C

check_init() (Entrez method) clear_internal_node_names() (PhyloTree method) close() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) (DatabaseUNITE method) commit_to_storage() (DatabaseStorageManager method) complement() (Nucleotide method) compress_storage() (DatabaseStorageManager method)

compute() (Marker method) copy() (BiomeAssembly method) (BiomeSurvey method) (FrequencyTable method) (MultiSequence method) (Nucleotide method) (PhyloTree method) (RepPhylogeny method) (RepSequence method) (RepTaxonomy method) (SampleMetadata method)

D

DatabaseGreengenes (class in pmaf.database) DatabaseGTDB (class in pmaf.database) DatabaseOTL (class in pmaf.database) DatabaseSILVA (class in pmaf.database) DatabaseStorageManager (class in pmaf.database) DatabaseUNITE (class in pmaf.database) docker DockerAccessionMedium (class in pmaf.pipe.agents.dockers) DockerIdentifierMedium (class in pmaf.pipe.agents.dockers)

DockerPhylogenyMedium (class in pmaf.pipe.agents.dockers) DockerSequenceMedium (class in pmaf.pipe.agents.dockers) DockerTaxonomyMedium (class in pmaf.pipe.agents.dockers) drop_feature_by_id() (RepTaxonomy method) drop_features_by_id() (FrequencyTable method) drop_features_without_counts() (FrequencyTable method) drop_features_without_ranks() (RepTaxonomy method) drop_features_without_taxa() (RepTaxonomy method) drop_sample_by_id() (SampleMetadata method) drop_samples_by_id() (FrequencyTable method)

E

embed_specs() (Marker method) Entrez (class in pmaf.remote) estimate() (BranchestERABLE method) (BranchestFastTree2 method) export() (BiomeAssembly method) (FrequencyTable method) (RepPhylogeny method) (RepSequence method) (RepTaxonomy method) (SampleMetadata method)

F

factor Factor16S (class in pmaf.pipe.factors) filter_genes_from_future_table() (Entrez method) find_features_by_pattern() (RepTaxonomy method) find_features_without_taxa() (RepTaxonomy method) find_rid_by_tid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) (DatabaseUNITE method) find_sub_tids_by_tid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) (DatabaseUNITE method)

find_tid_by_rid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) (DatabaseUNITE method) FrequencyTable (class in pmaf.biome) from_biom() (FrequencyTable class method) (RepTaxonomy class method) (SampleMetadata class method) from_buckled() (MultiSequence class method) from_csv() (FrequencyTable class method) (RepTaxonomy class method) (SampleMetadata class method)

G

get_accession_by_identifier() (MediatorLocalAccessionMixin method) (NCBIMediator method) get_accession_by_rid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) (DatabaseUNITE method) get_accession_by_tid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) (DatabaseUNITE method) get_alignment_by_rid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseSILVA method) (DatabaseUNITE method) get_alignment_by_tid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseSILVA method) (DatabaseUNITE method) get_annotated_tree() (RepPhylogeny method) get_ascii_art() (PhyloTree method) (RepPhylogeny method) get_avail_ranks() (DockerTaxonomyMedium method) get_chromosome_id_by_genome_id() (Entrez method) get_consensus() (MultiSequence method) get_element_data_by_ids() (DatabaseStorageManager method) get_fasta_sequence_by_param() (Entrez method) get_feature_ids() (BiomeAssembly method) (BiomeSurvey method) (FrequencyTable method) (RepPhylogeny method) (RepSequence method) (RepTaxonomy method) get_gene_features_by_chromosome_id() (Entrez method) get_genome_id_by_taxid() (Entrez method) get_identifier_by_accession() (MediatorLocalAccessionMixin method) (NCBIMediator method) get_identifier_by_phylogeny() (MediatorLocalPhylogenyMixin method) get_identifier_by_sequence() (MediatorLocalSequenceMixin method) (NCBIMediator method) get_identifier_by_taxonomy() (MediatorLocalTaxonomyMixin method) (NCBIMediator method) get_index_by_element() (DatabaseStorageManager method) get_iter() (MultiSequence method) get_iterator() (DockerAccessionMedium method) (DockerIdentifierMedium method) (DockerPhylogenyMedium method) (DockerSequenceMedium method) (DockerTaxonomyMedium method) get_lineage_by_id() (RepTaxonomy method) get_lineage_by_rid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) (DatabaseUNITE method) get_lineage_by_tid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) (DatabaseUNITE method) get_mcra_for_nodes() (PhyloTree method) get_newick_str() (PhyloTree method) get_node_by_name() (PhyloTree method) get_node_names() (DockerPhylogenyMedium method)

get_outputs() (Marker method) get_phylogeny_by_identifier() (MediatorLocalPhylogenyMixin method) get_records() (DockerSequenceMedium method) get_request_logs() (Entrez method) get_sample_ids() (BiomeAssembly method) (BiomeSurvey method) (FrequencyTable method) (SampleMetadata method) get_sequence_by_identifier() (MediatorLocalSequenceMixin method) (NCBIMediator method) get_sequence_by_rid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseSILVA method) (DatabaseUNITE method) get_sequence_by_tid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseSILVA method) (DatabaseUNITE method) get_stats() (DockerSequenceMedium method) get_stats_by_rid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) (DatabaseUNITE method) get_stats_by_tid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) (DatabaseUNITE method) get_string_as() (MultiSequence method) (Nucleotide method) get_subset() (BiomeAssembly method) (DockerAccessionMedium method) (DockerIdentifierMedium method) (DockerPhylogenyMedium method) (DockerSequenceMedium method) (DockerTaxonomyMedium method) (FrequencyTable method) (MultiSequence method) (RepPhylogeny method) (RepSequence method) (RepTaxonomy method) (SampleMetadata method) get_taxid_by_query() (Entrez method) get_taxonomy_by_id() (RepTaxonomy method) get_taxonomy_by_identifier() (MediatorLocalTaxonomyMixin method) (NCBIMediator method) get_taxonomy_by_rank() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) (DatabaseUNITE method) get_taxonomy_by_rid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) (DatabaseUNITE method) get_taxonomy_by_tid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) (DatabaseUNITE method) get_tip_names() (DockerPhylogenyMedium method) get_tree() (DockerPhylogenyMedium method) get_variables_by_id() (SampleMetadata method)

H

hdf5

I

imprint_database() (DatabaseStorageManager method) infer_topology_by_rid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method)

infer_topology_by_tid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) initiate_memory_cache() (DatabaseStorageManager method) IUPAC

L

ladderize() (PhyloTree method)

LocalMediator() (in module pmaf.pipe.agents.mediators)

M

Marker (class in pmaf.pipe.markers) mediator MediatorLocalAccessionMixin (class in pmaf.pipe.agents.mediators._local._components) MediatorLocalPhylogenyMixin (class in pmaf.pipe.agents.mediators._local._components) MediatorLocalSequenceMixin (class in pmaf.pipe.agents.mediators._local._components) MediatorLocalTaxonomyMixin (class in pmaf.pipe.agents.mediators._local._components) merge_duplicated_features() (RepTaxonomy method) merge_features_by_map() (FrequencyTable method) merge_features_by_rank() (RepTaxonomy method) merge_nodes() (PhyloTree method) merge_samples_by_map() (FrequencyTable method) merge_samples_by_variable() (SampleMetadata method) Miner (class in pmaf.pipe.agents.miners) module pmaf pmaf.alignment pmaf.biome pmaf.database pmaf.internal pmaf.internal.io pmaf.phylo pmaf.phylo.branchest pmaf.phylo.builders pmaf.pipe pmaf.pipe.agents pmaf.pipe.agents.dockers pmaf.pipe.agents.mediators pmaf.pipe.agents.miners pmaf.pipe.factors pmaf.pipe.markers pmaf.pipe.specs pmaf.remote pmaf.sequence

MRCA MSA MultiSequence (class in pmaf.sequence) MultiSequenceAligner (class in pmaf.alignment)

N

NCBI NCBIMediator (class in pmaf.pipe.agents.mediators)

next() (Marker method) Nucleotide (class in pmaf.sequence)

P

PhyloTree (class in pmaf.phylo) pmaf module pmaf.alignment module pmaf.biome module pmaf.database module pmaf.internal module pmaf.internal.io module pmaf.phylo module pmaf.phylo.branchest module pmaf.phylo.builders module pmaf.pipe module pmaf.pipe.agents module pmaf.pipe.agents.dockers module

pmaf.pipe.agents.mediators module pmaf.pipe.agents.miners module pmaf.pipe.factors module pmaf.pipe.markers module pmaf.pipe.specs module pmaf.remote module pmaf.sequence module prune_by_ids() (PhyloTree method) prune_tree_by_rid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) prune_tree_by_tid() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method)

R

read() (Nucleotide class method) reconfig() (MediatorLocalAccessionMixin method) (MediatorLocalPhylogenyMixin method) (MediatorLocalSequenceMixin method) (MediatorLocalTaxonomyMixin method) (NCBIMediator method) remove_node() (PhyloTree method) remove_node_by_name() (PhyloTree method) rename_samples() (FrequencyTable method) (SampleMetadata method) render() (PhyloTree method) render_art() (RepPhylogeny method)

replace_nan_with() (FrequencyTable method) replace_nodes_by_map() (PhyloTree method) RepPhylogeny (class in pmaf.biome) RepSequence (class in pmaf.biome) RepTaxonomy (class in pmaf.biome) resolve_polytomy() (PhyloTree method) (RepPhylogeny method) restore_buckle() (MultiSequence method) (Nucleotide method) retrieve_data_by_element() (DatabaseStorageManager method) rids rRNA

S

SampleMetadata (class in pmaf.biome) SequenceIO (class in pmaf.internal.io) shutdown() (DatabaseStorageManager method)

singleton sort_by_name() (PhyloTree method) spec subs

T

tab take_rids_by_rank() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) (DatabaseUNITE method) take_tids_by_rank() (DatabaseGreengenes method) (DatabaseGTDB method) (DatabaseOTL method) (DatabaseSILVA method) (DatabaseUNITE method) taxid

tids to_array() (DockerIdentifierMedium method) to_assembly() (BiomeSurvey method) to_dataframe() (DockerTaxonomyMedium method) to_identifier_by_src() (DockerAccessionMedium method) to_multiseq() (DockerSequenceMedium method) (RepSequence method) to_otu_table() (BiomeAssembly method) to_skbio() (PhyloTree method) to_skbio_msa() (MultiSequence method) transform_to_relative_abundance() (FrequencyTable method) TreeBuilderFastTree2 (class in pmaf.phylo.builders)

U

unbuckle_uid() (Nucleotide method)

unroot() (PhyloTree method)

V

validate_storage() (DatabaseStorageManager static method) verify_docker() (Miner method) verify_factor() (MediatorLocalAccessionMixin method) (MediatorLocalPhylogenyMixin method) (MediatorLocalSequenceMixin method) (MediatorLocalTaxonomyMixin method) (NCBIMediator method)

W

wrap_meta() (DockerAccessionMedium method) (DockerIdentifierMedium method) (DockerPhylogenyMedium method) (DockerSequenceMedium method) (DockerTaxonomyMedium method)

write() (MultiSequence method) (Nucleotide method) (PhyloTree method) (RepPhylogeny method) write_otu_table() (BiomeAssembly method)

Y

yield_accession_by_identifier() (Miner method) yield_identifier_by_docker() (Miner method)

yield_phylogeny_by_identifier() (Miner method) yield_sequence_by_identifier() (Miner method) yield_taxonomy_by_identifier() (Miner method)