Index

_

__repr__() (autometa.taxonomy.ncbi.NCBI method)

__str__() (autometa.common.exceptions.DatabaseOutOfSyncError method) (autometa.taxonomy.ncbi.NCBI method)

A

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.hmmer) (in module autometa.common.external.prodigal) annotate_sequential() (in module autometa.common.external.hmmer) (in module autometa.common.external.prodigal) assign() (in module autometa.taxonomy.vote) autometa (module) autometa.binning (module) autometa.binning.summary (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.hmmer (module) autometa.common.external.prodigal (module) autometa.common.external.samtools (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.lca (module) autometa.taxonomy.majority_vote (module) autometa.taxonomy.ncbi (module) autometa.taxonomy.vote (module) 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.ncbi.NCBI attribute) ChecksumMismatchError compare_checksums() (autometa.config.databases.Databases method)

configure() (autometa.config.databases.Databases method) (in module autometa.config.environ) contigs_from_headers() (in module autometa.common.external.prodigal) convert_sseqids_to_taxids() (autometa.taxonomy.lca.LCA method) convert_taxid_dtype() (autometa.taxonomy.ncbi.NCBI method)

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_markers() (autometa.config.databases.Databases method) download_missing() (autometa.config.databases.Databases method) download_ncbi_files() (autometa.config.databases.Databases method)

E

ExternalToolError

extract_taxdump() (autometa.config.databases.Databases method)

F

file_length() (in module autometa.common.utilities) filter_markers() (in module autometa.common.external.hmmer) find_executables() (in module autometa.config.environ) fix_invalid_checksums() (autometa.config.databases.Databases method)

format_nr() (autometa.config.databases.Databases method) 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_config() (in module autometa.config.utilities)

get_lineage_dataframe() (autometa.taxonomy.ncbi.NCBI method) 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_versions() (in module autometa.config.environ) gunzip() (in module autometa.common.utilities)

H

hmmpress() (in module autometa.common.external.hmmer) (in module autometa.config.environ)

hmmscan() (in module autometa.common.external.hmmer) (in module autometa.config.environ) hmmsearch() (in module autometa.config.environ)

I

internet_is_connected() (autometa.config.databases.Databases method)

is_common_ancestor() (autometa.taxonomy.ncbi.NCBI method) is_consistent_with_other_orfs() (in module autometa.taxonomy.majority_vote)

L

largest_seq (autometa.common.metagenome.Metagenome attribute), [1] 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), [1] level (autometa.taxonomy.lca.LCA attribute) level_fp (autometa.taxonomy.lca.LCA attribute) lineage() (autometa.taxonomy.ncbi.NCBI method) load() (in module autometa.common.markers) lowest_majority() (in module autometa.taxonomy.majority_vote)

M

main() (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.hmmer) (in module autometa.common.external.prodigal) (in module autometa.common.external.samtools) (in module autometa.common.markers) (in module autometa.common.metagenome) (in module autometa.config.databases) (in module autometa.config.utilities) (in module autometa.taxonomy.lca) (in module autometa.taxonomy.majority_vote) (in module autometa.taxonomy.vote)

majority_vote() (in module autometa.taxonomy.majority_vote) make_length_table() (in module autometa.common.coverage) make_pickle() (in module autometa.common.utilities) makedatabase() (in module autometa.common.external.diamond) Metagenome (class in autometa.common.metagenome)

N

name() (autometa.taxonomy.ncbi.NCBI method) NCBI (class in autometa.taxonomy.ncbi)

ncbi_dir (autometa.config.databases.Databases attribute) normalize() (in module autometa.common.coverage) nseqs (autometa.common.metagenome.Metagenome attribute), [1]

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.ncbi.NCBI 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_merged() (autometa.taxonomy.ncbi.NCBI method) parse_names() (autometa.taxonomy.ncbi.NCBI method)

parse_nodes() (autometa.taxonomy.ncbi.NCBI method) 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.ncbi.NCBI method) rank_taxids() (in module autometa.taxonomy.majority_vote) read_checksum() (in module autometa.common.utilities)

reduce_taxids_to_lcas() (autometa.taxonomy.lca.LCA method) run() (in module autometa.common.external.bowtie) (in module autometa.common.external.prodigal)

S

samtools() (in module autometa.config.environ) satisfied() (autometa.config.databases.Databases method) SECTIONS (autometa.config.databases.Databases attribute) seqrecords (autometa.common.metagenome.Metagenome attribute), [1] sequences (autometa.common.metagenome.Metagenome attribute), [1]

set_home_dir() (in module autometa.config.utilities) size (autometa.common.metagenome.Metagenome attribute), [1] 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)

timeit() (in module autometa.common.utilities) tour (autometa.taxonomy.lca.LCA attribute) tour_fp (autometa.taxonomy.lca.LCA attribute)

U

unpickle() (in module autometa.common.utilities)

untar() (in module autometa.common.utilities) update_config() (in module autometa.config.utilities)

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_votes() (in module autometa.taxonomy.majority_vote)