Index

Symbols

--db gambit command line option --ids gambit-signatures-create command line option gambit-signatures-info command line option --json gambit-signatures-info command line option --meta-json gambit-signatures-create command line option --outfmt gambit-query command line option --output gambit-query command line option gambit-signatures-create command line option --prefix gambit-signatures-create command line option --pretty gambit-signatures-info command line option --sigfile gambit-query command line option

-d gambit command line option -f gambit-query command line option -i gambit-signatures-create command line option gambit-signatures-info command line option -j gambit-signatures-info command line option -k gambit-signatures-create command line option -m gambit-signatures-create command line option -o gambit-query command line option gambit-signatures-create command line option -p gambit-signatures-create command line option gambit-signatures-info command line option -s gambit-query command line option

_

__bool__() (gambit.sigs.hdf5.HDF5Signatures method) __eq__() (gambit.sigs.base.AbstractSignatureArray method) __from_json__() (gambit.util.json.Jsonable class method) __init__() (gambit.classify.ClassifierResult method) (gambit.classify.GenomeMatch method) (gambit.cli.common.CLIContext method) (gambit.db.models.AnnotatedGenome method) (gambit.db.models.Genome method) (gambit.db.models.ReferenceGenomeSet method) (gambit.db.models.Taxon method) (gambit.db.refdb.ReferenceDatabase method) (gambit.kmers.KmerMatch method) (gambit.kmers.KmerSpec method) (gambit.query.QueryInput method) (gambit.query.QueryParams method) (gambit.query.QueryResultItem method) (gambit.query.QueryResults method) (gambit.results.archive.ResultsArchiveReader method) (gambit.results.archive.ResultsArchiveWriter method) (gambit.results.base.BaseJSONResultsExporter method) (gambit.results.csv.CSVResultsExporter method) (gambit.results.json.JSONResultsExporter method) (gambit.seq.SequenceFile method) (gambit.sigs.base.AnnotatedSignatures method) (gambit.sigs.base.SignatureArray method) (gambit.sigs.base.SignatureList method) (gambit.sigs.base.SignaturesMeta method) (gambit.sigs.calc.ArrayAccumulator method) (gambit.sigs.calc.SetAccumulator method) (gambit.sigs.hdf5.HDF5Signatures method), [1] (gambit.util.io.ClosingIterator method) (gambit.util.progress.ClickProgressMeter method) (gambit.util.progress.ProgressConfig method) (gambit.util.progress.ProgressIterator method) (gambit.util.progress.TestProgressMeter method) (gambit.util.progress.TqdmProgressMeter method)

__to_json__() (gambit.util.json.Jsonable method)

A

absolute() (gambit.seq.SequenceFile method) AbstractProgressMeter (class in gambit.util.progress) AbstractResultsExporter (class in gambit.results.base) AbstractSignatureArray (class in gambit.sigs.base), [1] accumulate_kmers() (in module gambit.sigs.calc) add() (gambit.sigs.calc.ArrayAccumulator method) (gambit.sigs.calc.SetAccumulator method) add_kmer() (gambit.sigs.calc.KmerAccumulator method)

AdvancedIndexingMixin (class in gambit.util.indexing) ancestor_of_rank() (gambit.db.models.Taxon method) ancestors() (gambit.db.models.Taxon method) AnnotatedGenome (class in gambit.db.models) AnnotatedSignatures (class in gambit.sigs.base) annotations (gambit.db.models.Genome attribute) ArrayAccumulator (class in gambit.sigs.calc) asdict_method() (in module gambit.results.base)

B

base_genomes (gambit.db.models.ReferenceGenomeSet attribute) BaseJSONResultsExporter (class in gambit.results.base)

bounds (gambit.sigs.base.ConcatenatedSignatureArray attribute) (gambit.sigs.base.SignatureArray attribute)

C

calc_file_signature() (in module gambit.sigs.calc) calc_file_signatures() (in module gambit.sigs.calc) calc_signature() (in module gambit.sigs.calc) callable (gambit.util.progress.ProgressConfig attribute) can_convert() (in module gambit.sigs.convert) capture_progress() (in module gambit.util.progress) check_can_convert() (in module gambit.sigs.convert) check_params_group() (in module gambit.cli.common) check_progress() (in module gambit.util.progress) children (gambit.db.models.Taxon attribute) chunk_slices() (in module gambit.util.misc) chunksize (gambit.query.QueryParams attribute) classifier_result (gambit.query.QueryResultItem attribute) ClassifierResult (class in gambit.classify) classify() (in module gambit.classify) classify_strict (gambit.query.QueryParams attribute) clear() (gambit.sigs.calc.ArrayAccumulator method) (gambit.sigs.calc.SetAccumulator method) ClickProgressMeter (class in gambit.util.progress) CLIContext (class in gambit.cli.common) close() (gambit.sigs.hdf5.HDF5Signatures method), [1] (gambit.util.io.ClosingIterator method) (gambit.util.progress.AbstractProgressMeter method) (gambit.util.progress.ClickProgressMeter method) (gambit.util.progress.NullProgressMeter method) (gambit.util.progress.TestProgressMeter method) (gambit.util.progress.TqdmProgressMeter method)

closed (gambit.util.io.ClosingIterator attribute) (gambit.util.progress.AbstractProgressMeter attribute) closest_genomes (gambit.query.QueryResultItem attribute) closest_match (gambit.classify.ClassifierResult attribute) ClosingIterator (class in gambit.util.io) common_ancestors() (gambit.db.models.Taxon class method) compare_classifier_results() (in module gambit.classify) compare_genome_matches() (in module gambit.classify) compare_result_items() (in module gambit.query) compression (gambit.seq.SequenceFile attribute) ConcatenatedSignatureArray (class in gambit.sigs.base) config() (gambit.util.progress.AbstractProgressMeter class method) consensus_taxon() (in module gambit.classify) convert() (gambit.query.QueryInput class method) convert_dense() (in module gambit.sigs.convert) convert_sparse() (in module gambit.sigs.convert) cores_param() (in module gambit.cli.common) create() (gambit.sigs.hdf5.HDF5Signatures class method), [1] (gambit.util.progress.AbstractProgressMeter class method) (gambit.util.progress.ClickProgressMeter class method) (gambit.util.progress.NullProgressMeter class method) (gambit.util.progress.ProgressConfig method) (gambit.util.progress.TestProgressMeter class method) (gambit.util.progress.TqdmProgressMeter class method) CSVResultsExporter (class in gambit.results.csv) CURRENT_FMT_VERSION (in module gambit.sigs.hdf5) current_head() (in module gambit.db.migrate) current_revision() (in module gambit.db.migrate)

D

db_path (gambit.cli.common.CLIContext attribute) default_accumulator() (in module gambit.sigs.calc) DEFAULT_KMERSPEC (in module gambit.kmers) default_progress_cls() (in module gambit.util.progress) dense_to_sparse() (in module gambit.sigs.convert) depth() (gambit.db.models.Taxon method) descendants() (gambit.db.models.Taxon method) description (gambit.db.models.AnnotatedGenome attribute) (gambit.db.models.Genome attribute) (gambit.db.models.ReferenceGenomeSet attribute) (gambit.db.models.Taxon attribute) (gambit.sigs.base.SignaturesMeta attribute)

dirpath() (in module gambit.cli.common) discard() (gambit.sigs.calc.ArrayAccumulator method) (gambit.sigs.calc.SetAccumulator method) distance (gambit.classify.GenomeMatch attribute) distance_threshold (gambit.db.models.Taxon attribute) DNASeq (in module gambit.seq) DNASeqBytes (in module gambit.seq) dtype (gambit.sigs.base.AbstractSignatureArray attribute), [1] dump() (in module gambit.util.json) dump_signatures() (in module gambit.sigs.base) dump_signatures_hdf5() (in module gambit.sigs.hdf5) dumps() (in module gambit.util.json)

E

empty_to_none() (in module gambit.sigs.hdf5) engine (gambit.cli.common.CLIContext attribute) environment variable GAMBIT_DB_PATH, [1] error (gambit.classify.ClassifierResult attribute) export() (gambit.results.base.AbstractResultsExporter method) (gambit.results.base.BaseJSONResultsExporter method) (gambit.results.csv.CSVResultsExporter method)

export_to_buffer() (in module gambit.results.base) extra (gambit.db.models.Genome attribute) (gambit.db.models.ReferenceGenomeSet attribute) (gambit.db.models.Taxon attribute) (gambit.query.QueryResults attribute) (gambit.sigs.base.SignaturesMeta attribute)

F

file (gambit.query.QueryInput attribute) FilePath (in module gambit.util.io) filepath() (in module gambit.cli.common) find_kmers() (in module gambit.kmers) find_matches() (in module gambit.classify) FMT_VERSION_ATTR (in module gambit.sigs.hdf5)

fobj (gambit.util.io.ClosingIterator attribute) format (gambit.seq.SequenceFile attribute) format_opts (gambit.results.csv.CSVResultsExporter attribute) from_arrays() (gambit.sigs.base.SignatureArray class method) from_json() (in module gambit.util.json) from_paths() (gambit.seq.SequenceFile class method) full_indices() (gambit.kmers.KmerMatch method)

G

gambit command line option --db -d gambit-query command line option --outfmt --output --sigfile -f -o -s gambit-signatures-create command line option --ids --meta-json --output --prefix -i -k -m -o -p gambit-signatures-info command line option --ids --json --pretty -i -j -p gambit.classify module gambit.cli module gambit.cli.common module gambit.cli.debug module gambit.cli.query module gambit.cli.root module gambit.cli.signatures module gambit.db module, [1] gambit.db.migrate module gambit.db.models module gambit.db.refdb module gambit.db.sqla module gambit.kmers module gambit.metric module gambit.query module gambit.results module gambit.results.archive module gambit.results.base module

gambit.results.csv module gambit.results.json module gambit.seq module gambit.sigs module gambit.sigs.base module gambit.sigs.calc module gambit.sigs.convert module gambit.sigs.hdf5 module gambit.util.dev module gambit.util.indexing module gambit.util.io module gambit.util.json module gambit.util.misc module gambit.util.progress module gambit.util.typing module GAMBIT_DB_PATH gambit_version (gambit.query.QueryResults attribute) genbank_acc (gambit.db.models.AnnotatedGenome attribute) (gambit.db.models.Genome attribute) Genome (class in gambit.db.models) genome (gambit.classify.GenomeMatch attribute) (gambit.db.models.AnnotatedGenome attribute) genome_files_arg() (in module gambit.cli.common) genome_id (gambit.db.models.AnnotatedGenome attribute) genome_set (gambit.db.models.AnnotatedGenome attribute) (gambit.db.models.Taxon attribute) genome_set_id (gambit.db.models.AnnotatedGenome attribute) (gambit.db.models.Taxon attribute) GenomeMatch (class in gambit.classify) genomes (gambit.db.models.ReferenceGenomeSet attribute) (gambit.db.models.Taxon attribute) (gambit.db.refdb.ReferenceDatabase attribute) genomes_by_id() (in module gambit.db.refdb) genomes_by_id_subset() (in module gambit.db.refdb) genomeset (gambit.db.refdb.ReferenceDatabase attribute) (gambit.query.QueryResults attribute) get_alembic_config() (in module gambit.db.migrate) get_commit_info() (in module gambit.util.dev) get_database() (gambit.cli.common.CLIContext method) get_file_id() (in module gambit.cli.common) get_header() (gambit.results.csv.CSVResultsExporter method) get_progress() (in module gambit.util.progress) get_result_item() (in module gambit.query) get_row() (gambit.results.csv.CSVResultsExporter method) get_sequence_files() (in module gambit.cli.common) group (gambit.sigs.hdf5.HDF5Signatures attribute), [1] guess_compression() (in module gambit.util.io)

H

has_database (gambit.cli.common.CLIContext attribute) has_genome() (gambit.db.models.Taxon method)

has_genomes (gambit.cli.common.CLIContext attribute) has_signatures (gambit.cli.common.CLIContext attribute) HDF5Signatures (class in gambit.sigs.hdf5), [1]

I

id (gambit.db.models.Genome attribute) (gambit.db.models.ReferenceGenomeSet attribute) (gambit.db.models.Taxon attribute) (gambit.sigs.base.SignaturesMeta attribute) id_attr (gambit.sigs.base.SignaturesMeta attribute) ID_ATTRS (gambit.db.models.Genome attribute) ids (gambit.sigs.base.ReferenceSignatures attribute) idx_len (gambit.kmers.KmerSpec attribute) increment() (gambit.util.progress.AbstractProgressMeter method) (gambit.util.progress.ClickProgressMeter method) (gambit.util.progress.NullProgressMeter method) (gambit.util.progress.TestProgressMeter method) (gambit.util.progress.TqdmProgressMeter method) index_dtype (gambit.kmers.KmerSpec attribute) index_dtype() (in module gambit.kmers)

index_to_kmer() (in module gambit.kmers) init_db() (in module gambit.db.migrate) input (gambit.query.QueryResultItem attribute) insert() (gambit.sigs.base.SignatureList method) install_info (gambit.results.archive.ResultsArchiveWriter attribute) install_info() (in module gambit.util.dev) is_current_revision() (in module gambit.db.migrate) is_importable() (in module gambit.util.misc) is_optional() (in module gambit.util.typing) is_union() (in module gambit.util.typing) isleaf() (gambit.db.models.Taxon method) isroot() (gambit.db.models.Taxon method) items (gambit.query.QueryResults attribute) iter_progress() (in module gambit.util.progress) iterator (gambit.util.io.ClosingIterator attribute)

J

jaccard() (in module gambit.metric) jaccard_bits() (in module gambit.metric) jaccard_generic() (in module gambit.metric) jaccarddist() (in module gambit.metric) jaccarddist_array() (in module gambit.metric)

jaccarddist_matrix() (in module gambit.metric) jaccarddist_pairwise() (in module gambit.metric) join_list_human() (in module gambit.util.misc) Jsonable (class in gambit.util.json) JSONResultsExporter (class in gambit.results.json) JsonString (class in gambit.db.sqla)

K

k (gambit.kmers.KmerSpec attribute) key (gambit.db.models.AnnotatedGenome attribute) (gambit.db.models.Genome attribute) (gambit.db.models.ReferenceGenomeSet attribute) (gambit.db.models.Taxon attribute) kmer() (gambit.kmers.KmerMatch method) kmer_index() (gambit.kmers.KmerMatch method) kmer_indices() (gambit.kmers.KmerMatch method) kmer_to_index() (in module gambit.kmers)

kmer_to_index_rc() (in module gambit.kmers) KmerAccumulator (class in gambit.sigs.calc) KmerMatch (class in gambit.kmers) KmerSignature (in module gambit.sigs.base) KmerSpec (class in gambit.kmers) kmerspec (gambit.kmers.KmerMatch attribute) (gambit.sigs.base.AbstractSignatureArray attribute), [1] kspec_from_params() (in module gambit.cli.common) kspec_params() (in module gambit.cli.common) kw (gambit.util.progress.ProgressConfig attribute)

L

label (gambit.query.QueryInput attribute) lca() (gambit.db.models.Taxon class method) leaves() (gambit.db.models.Taxon method) lineage() (gambit.db.models.Taxon method) listfile_dir_param() (in module gambit.cli.common) listfile_param() (in module gambit.cli.common) load() (gambit.db.refdb.ReferenceDatabase class method) (in module gambit.util.json)

load_from_dir() (gambit.db.refdb.ReferenceDatabase class method) load_genomeset() (in module gambit.db.refdb) load_signatures() (in module gambit.sigs.base) load_signatures_hdf5() (in module gambit.sigs.hdf5) loads() (in module gambit.util.json) locate_files() (gambit.db.refdb.ReferenceDatabase class method)

M

make_shell_ns() (in module gambit.cli.debug) matching_taxon (gambit.classify.GenomeMatch attribute) matching_taxon() (in module gambit.classify) maybe_open() (in module gambit.util.io) meta (gambit.sigs.base.ReferenceSignatures attribute) module gambit.classify gambit.cli gambit.cli.common gambit.cli.debug gambit.cli.query gambit.cli.root gambit.cli.signatures gambit.db, [1] gambit.db.migrate gambit.db.models gambit.db.refdb gambit.db.sqla gambit.kmers gambit.metric gambit.query gambit.results gambit.results.archive gambit.results.base gambit.results.csv gambit.results.json gambit.seq gambit.sigs gambit.sigs.base gambit.sigs.calc gambit.sigs.convert gambit.sigs.hdf5 gambit.util.dev gambit.util.indexing gambit.util.io gambit.util.json gambit.util.misc gambit.util.progress gambit.util.typing

moveto() (gambit.util.progress.AbstractProgressMeter method) (gambit.util.progress.ClickProgressMeter method) (gambit.util.progress.NullProgressMeter method) (gambit.util.progress.TestProgressMeter method) (gambit.util.progress.TqdmProgressMeter method)

N

n (gambit.util.progress.AbstractProgressMeter attribute) name (gambit.db.models.ReferenceGenomeSet attribute) (gambit.db.models.Taxon attribute) (gambit.sigs.base.SignaturesMeta attribute) ncbi_db (gambit.db.models.AnnotatedGenome attribute) (gambit.db.models.Genome attribute) ncbi_id (gambit.db.models.AnnotatedGenome attribute) (gambit.db.models.Genome attribute) (gambit.db.models.Taxon attribute)

next_taxon (gambit.classify.ClassifierResult attribute) next_taxon() (gambit.classify.GenomeMatch method) nkmers() (in module gambit.kmers) none_to_empty() (in module gambit.sigs.hdf5) NUCLEOTIDES (in module gambit.seq) NullProgressMeter (class in gambit.util.progress) num_pairs() (in module gambit.metric)

O

only_genomeset() (in module gambit.db.models) open() (gambit.seq.SequenceFile method)

open_compressed() (in module gambit.util.io) organism (gambit.db.models.AnnotatedGenome attribute)

P

param_name_human() (in module gambit.cli.common) params (gambit.query.QueryResults attribute) params_by_name() (in module gambit.cli.common) parent (gambit.db.models.Taxon attribute) parent_id (gambit.db.models.Taxon attribute) parse() (gambit.seq.SequenceFile method) path (gambit.seq.SequenceFile attribute) pos (gambit.kmers.KmerMatch attribute) predicted_taxon (gambit.classify.ClassifierResult attribute) prefix (gambit.kmers.KmerSpec attribute)

prefix_len (gambit.kmers.KmerSpec attribute) prefix_str (gambit.kmers.KmerSpec attribute) pretty (gambit.results.base.BaseJSONResultsExporter attribute) primary_match (gambit.classify.ClassifierResult attribute) print_table() (in module gambit.cli.common) print_tree() (gambit.db.models.Taxon method) progress_config() (in module gambit.util.progress) progress_param() (in module gambit.cli.common) ProgressConfig (class in gambit.util.progress) ProgressFactoryFunc (in module gambit.util.progress) ProgressIterator (class in gambit.util.progress)

Q

query() (in module gambit.query) query_parse() (in module gambit.query) QueryInput (class in gambit.query)

QueryParams (class in gambit.query) QueryResultItem (class in gambit.query) QueryResults (class in gambit.query)

R

rank (gambit.db.models.Taxon attribute) read() (gambit.results.archive.ResultsArchiveReader method) read_lines() (in module gambit.util.io) read_metadata() (in module gambit.sigs.hdf5) ReadOnlySession (class in gambit.db.sqla) ReferenceDatabase (class in gambit.db.refdb) ReferenceGenomeSet (class in gambit.db.models) ReferenceSignatures (class in gambit.sigs.base) refseq_acc (gambit.db.models.AnnotatedGenome attribute) (gambit.db.models.Genome attribute) register() (in module gambit.util.progress) register_hooks() (in module gambit.util.json) register_structure_hook_notype() (in module gambit.util.json) REGISTRY (in module gambit.util.progress)

report (gambit.db.models.Taxon attribute) report_closest (gambit.query.QueryParams attribute) report_taxon (gambit.query.QueryResultItem attribute) reportable_taxon() (in module gambit.db.models) require_database() (gambit.cli.common.CLIContext method) require_genomes() (gambit.cli.common.CLIContext method) require_signatures() (gambit.cli.common.CLIContext method) ResultsArchiveReader (class in gambit.results.archive) ResultsArchiveWriter (class in gambit.results.archive) revcomp() (in module gambit.seq) reverse (gambit.kmers.KmerMatch attribute) root() (gambit.db.models.Taxon method) root_context (gambit.cli.common.CLIContext attribute) root_taxa() (gambit.db.models.ReferenceGenomeSet method)

S

seq (gambit.kmers.KmerMatch attribute) seq_to_bytes() (in module gambit.seq) SequenceFile (class in gambit.seq) Session (gambit.cli.common.CLIContext attribute) session (gambit.db.refdb.ReferenceDatabase attribute) (gambit.results.archive.ResultsArchiveReader attribute) SetAccumulator (class in gambit.sigs.calc) SHELL_MODULES (in module gambit.cli.debug) short_repr() (gambit.db.models.Taxon method) sig_indices (gambit.db.refdb.ReferenceDatabase attribute) sigarray_eq() (in module gambit.sigs.base) signature() (gambit.sigs.calc.ArrayAccumulator method) (gambit.sigs.calc.KmerAccumulator method) (gambit.sigs.calc.SetAccumulator method)

SignatureArray (class in gambit.sigs.base) SignatureList (class in gambit.sigs.base) signatures (gambit.cli.common.CLIContext attribute) (gambit.db.refdb.ReferenceDatabase attribute) SignaturesMeta (class in gambit.sigs.base) signaturesmeta (gambit.query.QueryResults attribute) sizeof() (gambit.sigs.base.AbstractSignatureArray method), [1] (gambit.sigs.base.ConcatenatedSignatureArray method) sizes() (gambit.sigs.base.AbstractSignatureArray method), [1] (gambit.sigs.base.ConcatenatedSignatureArray method) sparse_to_dense() (in module gambit.sigs.convert) strip_seq_file_ext() (in module gambit.cli.common) subtree_genomes() (gambit.db.models.Taxon method) success (gambit.classify.ClassifierResult attribute)

T

taxa (gambit.db.models.ReferenceGenomeSet attribute) Taxon (class in gambit.db.models) taxon (gambit.db.models.AnnotatedGenome attribute) taxon_id (gambit.db.models.AnnotatedGenome attribute) TestProgressMeter (class in gambit.util.progress) timestamp (gambit.query.QueryResults attribute) to_json() (gambit.results.archive.ResultsArchiveWriter method) (gambit.results.base.BaseJSONResultsExporter method) (gambit.results.json.JSONResultsExporter method) (in module gambit.util.json)

total (gambit.util.progress.AbstractProgressMeter attribute) total_len (gambit.kmers.KmerSpec attribute) TqdmProgressMeter (class in gambit.util.progress) traverse() (gambit.db.models.Taxon method) type_singledispatchmethod() (in module gambit.util.misc)

U

uninitialized() (gambit.sigs.base.SignatureArray class method) union_types() (in module gambit.util.typing)

unwrap_optional() (in module gambit.util.typing) update() (gambit.util.progress.ProgressConfig method) upgrade() (in module gambit.db.migrate)

V

validate_dna_seq_bytes() (in module gambit.seq) values (gambit.sigs.base.ConcatenatedSignatureArray attribute) (gambit.sigs.base.SignatureArray attribute)

version (gambit.db.models.ReferenceGenomeSet attribute) (gambit.sigs.base.SignaturesMeta attribute)

W

warn_duplicate_file_ids() (in module gambit.cli.common) warnings (gambit.classify.ClassifierResult attribute)

write_lines() (in module gambit.util.io) write_metadata() (in module gambit.sigs.hdf5)

Z

zip_strict() (in module gambit.util.misc)