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Autometa Python API
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Autometa modules
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Autometa
Index
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Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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Z
_
__repr__() (autometa.taxonomy.gtdb.GTDB method)
(autometa.taxonomy.ncbi.NCBI method)
__str__() (autometa.common.exceptions.DatabaseOutOfSyncError method)
(autometa.taxonomy.gtdb.GTDB method)
(autometa.taxonomy.ncbi.NCBI method)
A
add_clustering_runtime_summary_info() (in module autometa.binning.large_data_mode_loginfo)
add_embedding_runtime_summary_info() (in module autometa.binning.large_data_mode_loginfo)
add_metrics() (in module autometa.binning.utilities)
add_ranks() (in module autometa.taxonomy.vote)
aggregate_orfs() (in module autometa.common.external.prodigal)
align() (in module autometa.common.external.bowtie)
annotate_parallel() (in module autometa.common.external.hmmscan)
(in module autometa.common.external.prodigal)
annotate_sequential() (in module autometa.common.external.hmmscan)
(in module autometa.common.external.prodigal)
apply_binning_metrics_filter() (in module autometa.binning.utilities)
assess_assembly() (in module autometa.validation.cluster_process)
assign() (in module autometa.taxonomy.vote)
autometa
module
autometa.binning
module
autometa.binning.large_data_mode
module
autometa.binning.large_data_mode_loginfo
module
autometa.binning.recursive_dbscan
module
autometa.binning.summary
module
autometa.binning.utilities
module
autometa.common
module
autometa.common.coverage
module
autometa.common.exceptions
module
autometa.common.external
module
autometa.common.external.bedtools
module
autometa.common.external.bowtie
module
autometa.common.external.diamond
module
autometa.common.external.hmmscan
module
autometa.common.external.hmmsearch
module
autometa.common.external.prodigal
module
autometa.common.external.samtools
module
autometa.common.kmers
module
autometa.common.markers
module
autometa.common.metagenome
module
autometa.common.utilities
module
autometa.config
module
autometa.config.databases
module
autometa.config.environ
module
autometa.config.utilities
module
autometa.datasets
module
autometa.taxonomy
module
autometa.taxonomy.database
module
autometa.taxonomy.gtdb
module
autometa.taxonomy.lca
module
autometa.taxonomy.majority_vote
module
autometa.taxonomy.ncbi
module
autometa.taxonomy.vote
module
autometa.validation
module
autometa.validation.benchmark
module
autometa.validation.cami
module
autometa.validation.cluster_process
module
autometa.validation.datasets
module
autometa_clr() (in module autometa.common.kmers)
AutometaError
B
bedtools() (in module autometa.config.environ)
BinningError
blast() (in module autometa.common.external.diamond)
blast2lca() (autometa.taxonomy.lca.LCA method)
bowtie2() (in module autometa.config.environ)
build() (in module autometa.common.external.bowtie)
C
calc_checksum() (in module autometa.common.utilities)
CANONICAL_RANKS (autometa.taxonomy.database.TaxonomyDatabase attribute)
checkpoint() (in module autometa.binning.large_data_mode)
ChecksumMismatchError
cluster_by_taxon_partitioning() (in module autometa.binning.large_data_mode)
compare_checksums() (autometa.config.databases.Databases method)
compute_classification_metrics() (in module autometa.validation.benchmark)
compute_clustering_metrics() (in module autometa.validation.benchmark)
configure() (autometa.config.databases.Databases method)
(in module autometa.config.environ)
contigs_from_headers() (in module autometa.common.external.prodigal)
convert_accessions_to_taxids() (autometa.taxonomy.database.TaxonomyDatabase method)
(autometa.taxonomy.gtdb.GTDB method)
(autometa.taxonomy.ncbi.NCBI method)
convert_taxid_dtype() (autometa.taxonomy.database.TaxonomyDatabase method)
(autometa.taxonomy.ncbi.NCBI method)
count() (in module autometa.common.kmers)
create_gtdb_db() (in module autometa.taxonomy.gtdb)
D
DatabaseOutOfSyncError
Databases (class in autometa.config.databases)
describe() (autometa.common.metagenome.Metagenome method)
diamond() (in module autometa.config.environ)
disable (autometa.taxonomy.lca.LCA attribute)
download() (in module autometa.validation.datasets)
download_gtdb_files() (autometa.config.databases.Databases method)
download_markers() (autometa.config.databases.Databases method)
download_missing() (autometa.config.databases.Databases method)
download_ncbi_files() (autometa.config.databases.Databases method)
E
embed() (in module autometa.common.kmers)
evaluate_binning_classification() (in module autometa.validation.benchmark)
evaluate_classification() (in module autometa.validation.benchmark)
evaluate_clustering() (in module autometa.validation.benchmark)
ExternalToolError
extract_taxdump() (autometa.config.databases.Databases method)
F
file_length() (in module autometa.common.utilities)
filter_domtblout() (in module autometa.common.external.hmmsearch)
filter_taxonomy() (in module autometa.binning.utilities)
filter_tblout_markers() (in module autometa.common.external.hmmscan)
find_executables() (in module autometa.config.environ)
fix_invalid_checksums() (autometa.config.databases.Databases method)
format_genome_binning() (in module autometa.validation.cami)
format_nr() (autometa.config.databases.Databases method)
format_profiling() (in module autometa.validation.cami)
format_taxon_binning() (in module autometa.validation.cami)
format_total_times() (in module autometa.binning.large_data_mode_loginfo)
fragmentation_metric() (autometa.common.metagenome.Metagenome method)
(in module autometa.binning.summary)
from_spades_names() (in module autometa.common.coverage)
G
gc_content() (autometa.common.metagenome.Metagenome method)
genomecov() (in module autometa.common.external.bedtools)
get() (in module autometa.common.coverage)
(in module autometa.common.markers)
(in module autometa.taxonomy.vote)
get_agg_stats() (in module autometa.binning.summary)
get_biobox_format() (in module autometa.validation.cami)
get_categorical_labels() (in module autometa.validation.benchmark)
get_checkpoint_info() (in module autometa.binning.large_data_mode)
get_clusters() (in module autometa.binning.recursive_dbscan)
get_config() (in module autometa.config.utilities)
get_kmer_embedding() (in module autometa.binning.large_data_mode)
get_lineage_dataframe() (autometa.taxonomy.database.TaxonomyDatabase method)
get_loginfo() (in module autometa.binning.large_data_mode_loginfo)
get_metabin_stats() (in module autometa.binning.summary)
get_metabin_taxonomies() (in module autometa.binning.summary)
get_missing() (autometa.config.databases.Databases method)
get_remote_checksum() (autometa.config.databases.Databases method)
get_target_labels() (in module autometa.validation.benchmark)
get_versions() (in module autometa.config.environ)
GTDB (class in autometa.taxonomy.gtdb)
gunzip() (in module autometa.common.utilities)
H
hmmpress() (in module autometa.common.external.hmmscan)
(in module autometa.config.environ)
hmmscan() (in module autometa.config.environ)
hmmsearch() (in module autometa.config.environ)
I
init_kmers() (in module autometa.common.kmers)
internet_is_connected() (in module autometa.common.utilities)
is_common_ancestor() (autometa.taxonomy.database.TaxonomyDatabase method)
is_consistent_with_other_orfs() (in module autometa.taxonomy.majority_vote)
is_gz_file() (in module autometa.common.utilities)
L
Labels (class in autometa.validation.benchmark)
largest_seq (autometa.common.metagenome.Metagenome attribute)
(autometa.common.metagenome.Metagenome property)
LCA (class in autometa.taxonomy.lca)
lca() (autometa.taxonomy.lca.LCA method)
lca_prepared (autometa.taxonomy.lca.LCA attribute)
length_filter() (autometa.common.metagenome.Metagenome method)
length_weighted_gc (autometa.common.metagenome.Metagenome attribute)
(autometa.common.metagenome.Metagenome property)
level (autometa.taxonomy.lca.LCA attribute)
level_fp (autometa.taxonomy.lca.LCA attribute)
lineage() (autometa.taxonomy.database.TaxonomyDatabase method)
load() (in module autometa.common.kmers)
(in module autometa.common.markers)
lowest_majority() (in module autometa.taxonomy.majority_vote)
M
main() (in module autometa.binning.large_data_mode)
(in module autometa.binning.large_data_mode_loginfo)
(in module autometa.binning.recursive_dbscan)
(in module autometa.binning.summary)
(in module autometa.common.coverage)
(in module autometa.common.external.bedtools)
(in module autometa.common.external.bowtie)
(in module autometa.common.external.hmmscan)
(in module autometa.common.external.hmmsearch)
(in module autometa.common.external.prodigal)
(in module autometa.common.external.samtools)
(in module autometa.common.kmers)
(in module autometa.common.markers)
(in module autometa.common.metagenome)
(in module autometa.config.databases)
(in module autometa.config.utilities)
(in module autometa.taxonomy.gtdb)
(in module autometa.taxonomy.lca)
(in module autometa.taxonomy.majority_vote)
(in module autometa.taxonomy.vote)
(in module autometa.validation.benchmark)
(in module autometa.validation.cami)
(in module autometa.validation.cluster_process)
(in module autometa.validation.datasets)
majority_vote() (in module autometa.taxonomy.majority_vote)
make_pickle() (in module autometa.common.utilities)
makedatabase() (in module autometa.common.external.diamond)
Metagenome (class in autometa.common.metagenome)
module
autometa
autometa.binning
autometa.binning.large_data_mode
autometa.binning.large_data_mode_loginfo
autometa.binning.recursive_dbscan
autometa.binning.summary
autometa.binning.utilities
autometa.common
autometa.common.coverage
autometa.common.exceptions
autometa.common.external
autometa.common.external.bedtools
autometa.common.external.bowtie
autometa.common.external.diamond
autometa.common.external.hmmscan
autometa.common.external.hmmsearch
autometa.common.external.prodigal
autometa.common.external.samtools
autometa.common.kmers
autometa.common.markers
autometa.common.metagenome
autometa.common.utilities
autometa.config
autometa.config.databases
autometa.config.environ
autometa.config.utilities
autometa.datasets
autometa.taxonomy
autometa.taxonomy.database
autometa.taxonomy.gtdb
autometa.taxonomy.lca
autometa.taxonomy.majority_vote
autometa.taxonomy.ncbi
autometa.taxonomy.vote
autometa.validation
autometa.validation.benchmark
autometa.validation.cami
autometa.validation.cluster_process
autometa.validation.datasets
mp_counter() (in module autometa.common.kmers)
N
name() (autometa.taxonomy.database.TaxonomyDatabase method)
NCBI (class in autometa.taxonomy.ncbi)
ncbi_dir (autometa.config.databases.Databases attribute)
ncbi_is_connected() (in module autometa.common.utilities)
normalize() (in module autometa.common.kmers)
nseqs (autometa.common.metagenome.Metagenome attribute)
(autometa.common.metagenome.Metagenome property)
O
occurrence (autometa.taxonomy.lca.LCA attribute)
occurrence_fp (autometa.taxonomy.lca.LCA attribute)
orf_records_from_contigs() (in module autometa.common.external.prodigal)
P
parent() (autometa.taxonomy.database.TaxonomyDatabase method)
parse() (autometa.taxonomy.lca.LCA method)
(in module autometa.common.external.bedtools)
(in module autometa.common.external.diamond)
parse_args() (in module autometa.config.utilities)
parse_delnodes() (autometa.taxonomy.database.TaxonomyDatabase method)
(autometa.taxonomy.gtdb.GTDB method)
(autometa.taxonomy.ncbi.NCBI method)
parse_merged() (autometa.taxonomy.database.TaxonomyDatabase method)
(autometa.taxonomy.gtdb.GTDB method)
(autometa.taxonomy.ncbi.NCBI method)
parse_names() (autometa.taxonomy.database.TaxonomyDatabase method)
(autometa.taxonomy.gtdb.GTDB method)
(autometa.taxonomy.ncbi.NCBI method)
parse_nodes() (autometa.taxonomy.database.TaxonomyDatabase method)
(autometa.taxonomy.gtdb.GTDB method)
(autometa.taxonomy.ncbi.NCBI method)
pred (autometa.validation.benchmark.Labels attribute)
(autometa.validation.benchmark.Targets attribute)
prepare_lca() (autometa.taxonomy.lca.LCA method)
prepare_tree() (autometa.taxonomy.lca.LCA method)
preprocess_minimums() (autometa.taxonomy.lca.LCA method)
press_hmms() (autometa.config.databases.Databases method)
prodigal() (in module autometa.config.environ)
put_config() (in module autometa.config.utilities)
R
rank() (autometa.taxonomy.database.TaxonomyDatabase method)
rank_taxids() (in module autometa.taxonomy.majority_vote)
read_annotations() (in module autometa.binning.utilities)
read_checksum() (in module autometa.common.utilities)
read_domtblout() (in module autometa.common.external.hmmscan)
read_sseqid_to_taxid_table() (autometa.taxonomy.lca.LCA method)
read_tblout() (in module autometa.common.external.hmmscan)
record_counter() (in module autometa.common.kmers)
recursive_dbscan() (in module autometa.binning.recursive_dbscan)
recursive_hdbscan() (in module autometa.binning.recursive_dbscan)
reduce_taxids_to_lcas() (autometa.taxonomy.lca.LCA method)
reindex_bin_names() (in module autometa.binning.utilities)
run() (in module autometa.common.external.bowtie)
(in module autometa.common.external.hmmscan)
(in module autometa.common.external.prodigal)
run_command() (in module autometa.validation.cluster_process)
run_dbscan() (in module autometa.binning.recursive_dbscan)
run_hdbscan() (in module autometa.binning.recursive_dbscan)
S
samtools() (in module autometa.config.environ)
satisfied() (autometa.config.databases.Databases method)
search_genome_accessions() (autometa.taxonomy.gtdb.GTDB method)
search_prot_accessions() (autometa.taxonomy.ncbi.NCBI method)
SECTIONS (autometa.config.databases.Databases attribute)
seq_counter() (in module autometa.common.kmers)
seqrecords (autometa.common.metagenome.Metagenome attribute)
(autometa.common.metagenome.Metagenome property)
sequences (autometa.common.metagenome.Metagenome attribute)
(autometa.common.metagenome.Metagenome property)
set_home_dir() (in module autometa.config.utilities)
size (autometa.common.metagenome.Metagenome attribute)
(autometa.common.metagenome.Metagenome property)
sort() (in module autometa.common.external.samtools)
sparse (autometa.taxonomy.lca.LCA attribute)
sparse_fp (autometa.taxonomy.lca.LCA attribute)
T
TableFormatError
tarchive_results() (in module autometa.common.utilities)
target_names (autometa.validation.benchmark.Targets attribute)
Targets (class in autometa.validation.benchmark)
taxon_guided_binning() (in module autometa.binning.recursive_dbscan)
TaxonomyDatabase (class in autometa.taxonomy.database)
timeit() (in module autometa.common.utilities)
tour (autometa.taxonomy.lca.LCA attribute)
tour_fp (autometa.taxonomy.lca.LCA attribute)
true (autometa.validation.benchmark.Labels attribute)
(autometa.validation.benchmark.Targets attribute)
U
UNCLASSIFIED (autometa.taxonomy.database.TaxonomyDatabase attribute)
unpickle() (in module autometa.common.utilities)
untar() (in module autometa.common.utilities)
update_config() (in module autometa.config.utilities)
V
verify_databases() (autometa.taxonomy.gtdb.GTDB method)
W
write_checksum() (in module autometa.common.utilities)
write_cluster_records() (in module autometa.binning.summary)
write_lcas() (autometa.taxonomy.lca.LCA method)
write_ranks() (in module autometa.taxonomy.vote)
write_reports() (in module autometa.validation.benchmark)
write_results() (in module autometa.binning.utilities)
write_votes() (in module autometa.taxonomy.majority_vote)
Z
zero_pad_bin_names() (in module autometa.binning.utilities)
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