Index

_

__getitem__() (rotifer.db.core.BaseCursor method) (rotifer.db.delegator.SequentialDelegatorCursor method) (rotifer.db.local.ete3.TaxonomyCursor method) (rotifer.db.ncbi.entrez.GeneNeighborhoodCursor method) (rotifer.db.ncbi.entrez.SequenceCursor method) (rotifer.db.ncbi.GeneNeighborhoodCursor method) (rotifer.db.ncbi.TaxonomyCursor method) (rotifer.db.parallel.GeneNeighborhoodCursor method) (rotifer.db.parallel.SimpleParallelProcessCursor method) (rotifer.db.sql.sqlite3.GeneNeighborhoodCursor method) (rotifer.db.sql.sqlite3.IPGCursor method) (rotifer.db.uniprot.BaseUniProtDelegatorCursor method) (rotifer.db.uniprot.BaseUniProtRecordCursor method)

A

absorb_missing() (rotifer.db.delegator.DelegatorCursor method) action (class in rotifer.core.cli) action.add_stdin (class in rotifer.core.cli) action.autoload (class in rotifer.core.cli) action.autoopen (class in rotifer.core.cli) action.buffer_stdin (class in rotifer.core.cli) action.dict_options (class in rotifer.core.cli) action.dict_options_dev (class in rotifer.core.cli) action.extend (class in rotifer.core.cli)

add() (rotifer.core.cli.parser method) add_gembase_qualifiers() (in module rotifer.genome.utils) add_stdin_to_list_of_input_files() (rotifer.core.cli.action method) AF_link() (in module rotifer.db.uniprot.webapi.idmapping) af_to_seq() (in module rotifer.db.uniprot.webapi.idmapping) Annotatable (class in rotifer.pipeline) annotate() (rotifer.pipeline.Annotatable method) architecture() (in module rotifer.interval.utils) assemblies() (in module rotifer.db.ncbi)

B

backend_arguments() (rotifer.db.delegator.DelegatorCursor method) (rotifer.db.uniprot.BaseUniProtDelegatorCursor method) (rotifer.db.uniprot.FastaCursor method) BaseCursor (class in rotifer.db.core)

BaseSQLite3Cursor (class in rotifer.db.sql.sqlite3) BaseUniProtDelegatorCursor (class in rotifer.db.uniprot) BaseUniProtRecordCursor (class in rotifer.db.uniprot) best_ipgs() (in module rotifer.db.ncbi.utils) boundaries() (rotifer.genome.data.NeighborhoodDF method)

C

check_args() (in module rotifer.core.cli) check_databases() (rotifer.db.uniprot.BaseUniProtDelegatorCursor method) check_id_mapping_results_ready() (in module rotifer.db.uniprot.webapi.idmapping) check_response() (in module rotifer.db.uniprot.webapi.idmapping) CHECKSUM (rotifer.db.methods.MappingCursor attribute) checksum() (rotifer.db.methods.MappingCursor class method) checksums (rotifer.db.methods.MappingCursor property) chunks() (in module rotifer.core.functions) classification() (rotifer.db.uniprot.TaxonomyCursor method) cleanup() (rotifer.db.sql.sqlite3.BaseSQLite3Cursor method) clickhouse (class in rotifer.alchemy.connect) (class in rotifer.genome.db.clickhouse) cluster_neighbor (class in rotifer.cluster.cluster)

clustering() (rotifer.cluster.cluster.cluster_neighbor method) columns (rotifer.db.methods.IPGCursor property) (rotifer.db.methods.MappingCursor property) combine_batches() (in module rotifer.db.uniprot.webapi.idmapping) complement() (in module rotifer.interval.utils) connect() (rotifer.db.ncbi.ftp.connection method) connection (class in rotifer.db.ncbi.ftp) content_id() (rotifer.db.core.BaseCursor method) (rotifer.db.sql.sqlite3.BaseSQLite3Cursor method) content_of() (rotifer.db.delegator.DelegatorCursor method) CoreMethods (class in rotifer.core.methods) create() (rotifer.db.uniprot.BaseUniProtDelegatorCursor method) create_sources() (rotifer.db.sql.sqlite3.BaseSQLite3Cursor method)

D

dali_tsv() (in module rotifer.io.dali) database (class in rotifer.genome.database) databases() (rotifer.db.methods.MappingCursor method) (rotifer.db.uniprot.BaseUniProtDelegatorCursor method) (rotifer.db.uniprot.webapi.idmapping.MappingCursor method) databases_by_backend() (rotifer.db.uniprot.BaseUniProtDelegatorCursor method)

decode_results() (in module rotifer.db.uniprot.webapi.idmapping) default_block_rows() (in module rotifer.pandas) default_header() (in module rotifer.pandas) DelegatorCursor (class in rotifer.db.delegator) display_html_popup_from_file() (in module rotifer.view.functions) dotdict (class in rotifer.core.cli) (class in rotifer.core.functions)

E

elink() (in module rotifer.db.ncbi.entrez) emit() (rotifer.core.logger.TqdmLoggingHandler method)

empty() (rotifer.db.methods.MappingCursor method) (rotifer.db.uniprot.TaxonomyCursor method) extend_yaml() (in module rotifer.core.cli)

F

FastaCursor (class in rotifer.db.local.easel) (class in rotifer.db.ncbi) (class in rotifer.db.ncbi.entrez) (class in rotifer.db.uniprot) fetchall() (rotifer.db.core.BaseCursor method) (rotifer.db.delegator.SequentialDelegatorCursor method) (rotifer.db.local.ete3.TaxonomyCursor method) (rotifer.db.methods.GeneNeighborhoodCursor method) (rotifer.db.methods.GenomeFeaturesCursor method) (rotifer.db.methods.MappingCursor method) (rotifer.db.ncbi.entrez.IPGCursor method) (rotifer.db.ncbi.entrez.NucleotideFeaturesCursor method) (rotifer.db.ncbi.entrez.TaxonomyCursor method) (rotifer.db.ncbi.GeneNeighborhoodCursor method) (rotifer.db.ncbi.IPGCursor method) (rotifer.db.ncbi.TaxonomyCursor method) (rotifer.db.parallel.SimpleParallelProcessCursor method) (rotifer.db.sql.sqlite3.GeneNeighborhoodCursor method) (rotifer.db.sql.sqlite3.IPGCursor method) (rotifer.db.uniprot.TaxonomyCursor method) fetcher() (rotifer.db.local.easel.FastaCursor method) (rotifer.db.methods.GenomeCursor method) (rotifer.db.ncbi.entrez.SequenceCursor method) (rotifer.db.parallel.GeneNeighborhoodCursor method) (rotifer.db.parallel.SimpleParallelProcessCursor method) (rotifer.db.uniprot.webapi.idmapping.MappingCursor method)

fetchone() (rotifer.db.core.BaseCursor method) (rotifer.db.delegator.SequentialDelegatorCursor method) (rotifer.db.local.ete3.TaxonomyCursor method) (rotifer.db.ncbi.entrez.GeneNeighborhoodCursor method) (rotifer.db.ncbi.entrez.IPGCursor method) (rotifer.db.ncbi.GeneNeighborhoodCursor method) (rotifer.db.parallel.GeneNeighborhoodCursor method) (rotifer.db.parallel.SimpleParallelProcessCursor method) (rotifer.db.sql.sqlite3.GeneNeighborhoodCursor method) (rotifer.db.uniprot.BaseUniProtDelegatorCursor method) (rotifer.db.uniprot.BaseUniProtRecordCursor method) (rotifer.db.uniprot.TaxonomyCursor method) fields() (rotifer.db.uniprot.webapi.idmapping.MappingCursor method) FileInput (class in rotifer.io.fileinput) filter_nonoverlapping_regions() (in module rotifer.interval.utils) findDataFiles() (in module rotifer.core.functions) forget_source() (rotifer.db.sql.sqlite3.BaseSQLite3Cursor method) ftp_get() (rotifer.db.ncbi.ftp.connection method) ftp_ls() (rotifer.db.ncbi.ftp.connection method) ftp_open() (rotifer.db.ncbi.ftp.connection method) full_neighborhood() (rotifer.genome.data.NeighborhoodDF method)

G

genbank_to_uniprot() (in module rotifer.db.uniprot.webapi.idmapping) GenbankAssemblyFromFilename() (in module rotifer.genome.io) GeneNeighborhoodCursor (class in rotifer.db.methods) (class in rotifer.db.ncbi) (class in rotifer.db.ncbi.entrez) (class in rotifer.db.ncbi.ftp) (class in rotifer.db.ncbi.mirror) (class in rotifer.db.parallel) (class in rotifer.db.sql.sqlite3) genome_ids() (rotifer.db.methods.GeneNeighborhoodCursor method) genome_path() (rotifer.db.ncbi.ftp.GenomeCursor method) (rotifer.db.ncbi.mirror.GenomeCursor method) genome_report() (rotifer.db.ncbi.ftp.GenomeCursor method) (rotifer.db.ncbi.mirror.GenomeCursor method) GenomeCursor (class in rotifer.db.methods) (class in rotifer.db.ncbi) (class in rotifer.db.ncbi.ftp) (class in rotifer.db.ncbi.mirror) GenomeFeaturesCursor (class in rotifer.db.methods) (class in rotifer.db.ncbi) (class in rotifer.db.ncbi.ftp) (class in rotifer.db.ncbi.mirror) get_batch() (in module rotifer.db.uniprot.webapi.idmapping) get_data_frame_from_tsv_results() (in module rotifer.db.uniprot.webapi.idmapping)

get_id_mapping_results_link() (in module rotifer.db.uniprot.webapi.idmapping) get_id_mapping_results_search() (in module rotifer.db.uniprot.webapi.idmapping) get_id_mapping_results_stream() (in module rotifer.db.uniprot.webapi.idmapping) get_logger() (in module rotifer.core.logger) get_next_link() (in module rotifer.db.uniprot.webapi.idmapping) get_some_info() (in module rotifer.core.functions) get_xml_namespace() (in module rotifer.db.uniprot.webapi.idmapping) getids() (rotifer.db.core.BaseCursor method) (rotifer.db.local.easel.FastaCursor method) (rotifer.db.local.ete3.TaxonomyCursor method) (rotifer.db.methods.GeneNeighborhoodCursor method) (rotifer.db.methods.GenomeCursor method) (rotifer.db.methods.GenomeFeaturesCursor method) (rotifer.db.methods.IPGCursor method) (rotifer.db.methods.MappingCursor method) (rotifer.db.methods.SequenceCursor method) (rotifer.db.ncbi.entrez.NucleotideFeaturesCursor method) (rotifer.db.ncbi.entrez.TaxonomyCursor method) (rotifer.db.ncbi.TaxonomyCursor method) (rotifer.db.uniprot.FastaCursor method) (rotifer.db.uniprot.SequenceCursor method) (rotifer.db.uniprot.TaxonomyCursor method) getids2() (rotifer.db.ncbi.entrez.GeneNeighborhoodCursor method) gff() (in module rotifer.genome.io) group_strand() (rotifer.genome.data.NeighborhoodDF method)

H

has_table() (rotifer.db.sql.sqlite3.BaseSQLite3Cursor method)

hierarchy_to_dataframe() (in module rotifer.core.functions) hook_compressed_text() (in module rotifer.io.fileinput)

I

import_path() (in module rotifer.core.functions) input() (in module rotifer.io.fileinput) (rotifer.db.cli.rneighbors method) (rotifer.db.cli.sql method) insert() (rotifer.db.sql.sqlite3.GeneNeighborhoodCursor method) ipg_proteins() (rotifer.db.methods.GeneNeighborhoodCursor method) IPGCursor (class in rotifer.db.methods) (class in rotifer.db.ncbi) (class in rotifer.db.ncbi.entrez) (class in rotifer.db.sql.sqlite3)

ipgs_to_dict() (rotifer.db.methods.GeneNeighborhoodCursor method) ipgs_to_dicts() (in module rotifer.db.ncbi.utils) is_running_in_jupyter() (in module rotifer.view.functions) is_sequence() (rotifer.db.methods.MappingCursor static method)

L

lineage() (in module rotifer.taxonomy.utils) load() (rotifer.db.uniprot.BaseUniProtDelegatorCursor method) loadClasses() (in module rotifer.core.functions)

loadConfig() (in module rotifer.core.functions) loadPreferredTaxa() (in module rotifer.taxonomy.utils) log() (in module rotifer.core.log) logger() (in module rotifer.core.log)

M

MappingCursor (class in rotifer.db.methods) (class in rotifer.db.uniprot) (class in rotifer.db.uniprot.webapi.idmapping) md5() (in module rotifer.core.functions) merge_xml_results() (in module rotifer.db.uniprot.webapi.idmapping) missing (rotifer.db.core.BaseCursor property) missing_ids() (rotifer.db.core.BaseCursor method) module rotifer rotifer.alchemy rotifer.alchemy.connect rotifer.cluster rotifer.cluster.cluster rotifer.core rotifer.core.cli rotifer.core.functions rotifer.core.io.ftp rotifer.core.loadpath rotifer.core.log rotifer.core.logger rotifer.core.methods rotifer.core.time rotifer.db rotifer.db.cli rotifer.db.core rotifer.db.delegator rotifer.db.local rotifer.db.local.easel rotifer.db.local.ete3 rotifer.db.methods rotifer.db.ncbi rotifer.db.ncbi.entrez rotifer.db.ncbi.ftp rotifer.db.ncbi.mirror rotifer.db.ncbi.utils rotifer.db.parallel rotifer.db.sql rotifer.db.sql.sqlite3 rotifer.db.uniprot rotifer.db.uniprot.webapi rotifer.db.uniprot.webapi.idmapping rotifer.genome rotifer.genome.data rotifer.genome.database rotifer.genome.db.clickhouse rotifer.genome.db.postgres rotifer.genome.io rotifer.genome.utils rotifer.interval.utils rotifer.io.dali rotifer.io.fileinput rotifer.pandas rotifer.pandas.functions rotifer.pipeline rotifer.taxonomy rotifer.taxonomy.utils rotifer.view rotifer.view.functions

N

NeighborhoodDF (class in rotifer.genome.data) neighbors() (rotifer.genome.data.NeighborhoodDF method) not_kwargs() (in module rotifer.core.functions)

nucleotide2assembly() (in module rotifer.db.ncbi.entrez) nucleotide_ids() (rotifer.db.ncbi.entrez.GeneNeighborhoodCursor method) NucleotideFeaturesCursor (class in rotifer.db.ncbi.entrez)

O

open() (in module rotifer.core.io.ftp) (rotifer.genome.database.database method) open_compressed() (in module rotifer.core.functions) open_genome() (rotifer.db.ncbi.ftp.GenomeCursor method) (rotifer.db.ncbi.mirror.GenomeCursor method)

openread() (in module rotifer.core.functions) (rotifer.core.cli.action method) openread2() (rotifer.core.cli.action method) optimize_memory_usage() (in module rotifer.pandas.functions)

P

pad() (in module rotifer.pandas.functions) page_size (rotifer.db.uniprot.webapi.idmapping.MappingCursor attribute) parse() (in module rotifer.genome.io) parse_args() (rotifer.core.cli.parser method) parse_databases() (rotifer.db.methods.MappingCursor static method) parse_ids() (rotifer.db.core.BaseCursor method) (rotifer.db.methods.MappingCursor method) parser (class in rotifer.core.cli) parser() (rotifer.db.local.easel.FastaCursor method) (rotifer.db.methods.GenomeCursor method) (rotifer.db.methods.GenomeFeaturesCursor method) (rotifer.db.ncbi.entrez.GeneNeighborhoodCursor method) (rotifer.db.ncbi.entrez.IPGCursor method) (rotifer.db.ncbi.entrez.NucleotideFeaturesCursor method) (rotifer.db.ncbi.entrez.SequenceCursor method) (rotifer.db.ncbi.entrez.TaxonomyCursor method) (rotifer.db.parallel.GeneNeighborhoodCursor method) (rotifer.db.parallel.SimpleParallelProcessCursor method) (rotifer.db.uniprot.webapi.idmapping.MappingCursor method)

path (class in rotifer.core.loadpath) plt() (rotifer.cluster.cluster.cluster_neighbor method) postgres (class in rotifer.genome.db.postgres) print_everything() (in module rotifer.pandas.functions) print_progress_batches() (in module rotifer.db.uniprot.webapi.idmapping) progress_label (rotifer.db.core.BaseCursor property) proteins() (in module rotifer.db)

R

rdoc (class in rotifer.core.functions) read() (rotifer.io.fileinput.FileInput method) record_source() (rotifer.db.sql.sqlite3.BaseSQLite3Cursor method) recorded_source() (rotifer.db.sql.sqlite3.BaseSQLite3Cursor method) redundant() (rotifer.db.delegator.DelegatorCursor method) remove_missing() (rotifer.db.core.BaseCursor method) reset_cursors() (rotifer.db.delegator.DelegatorCursor method) resolve_fasta_path() (rotifer.db.uniprot.FastaCursor class method) resolve_sqlitedb() (rotifer.db.uniprot.BaseUniProtDelegatorCursor class method) restore_session() (in module rotifer.core.functions) rneighbors (class in rotifer.db.cli) rotifer module rotifer.alchemy module rotifer.alchemy.connect module rotifer.cluster module rotifer.cluster.cluster module rotifer.core module rotifer.core.cli module rotifer.core.functions module rotifer.core.io.ftp module rotifer.core.loadpath module rotifer.core.log module rotifer.core.logger module rotifer.core.methods module rotifer.core.time module rotifer.db module rotifer.db.cli module rotifer.db.core module rotifer.db.delegator module rotifer.db.local module rotifer.db.local.easel module rotifer.db.local.ete3 module rotifer.db.methods module rotifer.db.ncbi module

rotifer.db.ncbi.entrez module rotifer.db.ncbi.ftp module rotifer.db.ncbi.mirror module rotifer.db.ncbi.utils module rotifer.db.parallel module rotifer.db.sql module rotifer.db.sql.sqlite3 module rotifer.db.uniprot module rotifer.db.uniprot.webapi module rotifer.db.uniprot.webapi.idmapping module rotifer.genome module rotifer.genome.data module rotifer.genome.database module rotifer.genome.db.clickhouse module rotifer.genome.db.postgres module rotifer.genome.io module rotifer.genome.utils module rotifer.interval.utils module rotifer.io.dali module rotifer.io.fileinput module rotifer.pandas module rotifer.pandas.functions module rotifer.pipeline module rotifer.taxonomy module rotifer.taxonomy.utils module rotifer.view module rotifer.view.functions module rtime() (in module rotifer.core.time)

S

same_strand() (rotifer.genome.data.NeighborhoodDF method) save_session() (in module rotifer.core.functions) schema (rotifer.db.sql.sqlite3.BaseSQLite3Cursor property) select_neighbors() (rotifer.genome.data.NeighborhoodDF method) seqrecords_to_dataframe() (in module rotifer.genome.utils) sequence_checksums() (rotifer.db.methods.MappingCursor class method) SequenceCursor (class in rotifer.db.methods) (class in rotifer.db.ncbi) (class in rotifer.db.ncbi.entrez) (class in rotifer.db.uniprot) SequenceNameToAssembly() (in module rotifer.genome.io) SequentialDelegatorCursor (class in rotifer.db.delegator) series_to_compact_frequency() (rotifer.genome.data.NeighborhoodDF method) show_display_options() (in module rotifer.pandas.functions)

SimpleParallelProcessCursor (class in rotifer.db.parallel) source_version (rotifer.db.sql.sqlite3.BaseSQLite3Cursor property) sources_table (rotifer.db.sql.sqlite3.BaseSQLite3Cursor property) splitter() (rotifer.db.ncbi.entrez.GeneNeighborhoodCursor method) (rotifer.db.parallel.GeneNeighborhoodCursor method) (rotifer.db.parallel.SimpleParallelProcessCursor method) sql (class in rotifer.db.cli) standardize() (rotifer.db.uniprot.TaxonomyCursor method) store (rotifer.db.uniprot.BaseUniProtDelegatorCursor property) stored() (rotifer.db.sql.sqlite3.BaseSQLite3Cursor method) submit() (rotifer.db.sql.sqlite3.BaseSQLite3Cursor method) (rotifer.genome.database.database method) (rotifer.genome.db.clickhouse.clickhouse method) submit_id_mapping() (in module rotifer.db.uniprot.webapi.idmapping) supported() (rotifer.db.methods.MappingCursor method)

T

table_name() (rotifer.db.sql.sqlite3.BaseSQLite3Cursor method) tables (rotifer.db.sql.sqlite3.BaseSQLite3Cursor attribute) TaxonomyCursor (class in rotifer.db.local.ete3) (class in rotifer.db.ncbi) (class in rotifer.db.ncbi.entrez) (class in rotifer.db.uniprot)

to_blocks() (in module rotifer.pandas) to_color() (in module rotifer.pandas.functions) to_network() (in module rotifer.pandas) to_string() (in module rotifer.pandas) TqdmLoggingHandler (class in rotifer.core.logger)

U

UNIPROTKB (rotifer.db.methods.MappingCursor attribute) unsupported() (rotifer.db.methods.MappingCursor method) (rotifer.db.uniprot.BaseUniProtDelegatorCursor method)

update_database() (rotifer.db.local.ete3.TaxonomyCursor method) update_missing() (rotifer.db.core.BaseCursor method)

V

value_counts_full() (rotifer.genome.data.NeighborhoodDF method) version() (in module rotifer.core.cli)

vicinity() (rotifer.genome.data.NeighborhoodDF method) vmsg() (in module rotifer.core.functions)

W

who_is_calling() (in module rotifer.core.functions) worker() (rotifer.db.ncbi.entrez.GeneNeighborhoodCursor method) (rotifer.db.parallel.GeneNeighborhoodCursor method) (rotifer.db.parallel.SimpleParallelProcessCursor method)

writer() (rotifer.core.functions.rdoc method) (rotifer.genome.data.NeighborhoodDF method)

Y

yaml_search() (in module rotifer.core.functions)