Index

Symbols

--file magna-ncbi-download command line option --install-completion magna command line option

--show-completion magna command line option

_

__init__() (magna.gtdb.genome.GenomeDirs method)

A

accession (magna.gtdb.genome.Genome attribute)

AR122 (in module magna.gtdb.markers) AR53 (in module magna.gtdb.markers)

B

BAC120 (in module magna.gtdb.markers)

C

cache_file() (in module magna.util.disk) canonical_gid() (in module magna.util.accession) cds_path (magna.gtdb.genome.Genome attribute)

cds_seqio() (magna.gtdb.genome.Genome method) CMD magna-rq-conda command line option copy_file() (in module magna.util.disk)

D

df (magna.gtdb.metadata.GtdbMetadata attribute) (magna.gtdb.metadata.GtdbMetadataR202 attribute) (magna.gtdb.metadata.GtdbMetadataR95 attribute) (magna.gunc.GuncAllScores attribute) (magna.gunc.GuncMaxCssScores attribute)

dm_to_newick() (in module magna.util.tree) download_file() (in module magna.util.web) download_ncbi_assembly_file_to_disk() (in module magna.ncbi.web)

E

ENV magna-rq-conda command line option

F

fna_path (magna.gtdb.genome.Genome attribute)

fna_seqio() (magna.gtdb.genome.Genome method)

G

Genome (class in magna.gtdb.genome) GenomeDirs (class in magna.gtdb.genome) get() (magna.gtdb.genome.GenomeDirs method) get_batches() (in module magna.util.collection) get_file_size_fmt() (in module magna.util.disk) get_md5checksums() (in module magna.ncbi.web) get_ncbi_assembly_id() (in module magna.ncbi.web) get_ncbi_ftp_root() (in module magna.ncbi.web) GID magna-ncbi-download command line option GtdbMetadata (class in magna.gtdb.metadata) GtdbMetadataR202 (class in magna.gtdb.metadata) GtdbMetadataR202Arc (class in magna.gtdb.metadata) GtdbMetadataR202Bac (class in magna.gtdb.metadata)

GtdbMetadataR95 (class in magna.gtdb.metadata) GtdbMetadataR95Arc (class in magna.gtdb.metadata) GtdbMetadataR95Bac (class in magna.gtdb.metadata) GtdbRelease (class in magna.gtdb.enums) GtdbTree (class in magna.gtdb.tree) GtdbTreeR202Arc (class in magna.gtdb.tree) GtdbTreeR202Bac (class in magna.gtdb.tree) GtdbTreeR95Arc (class in magna.gtdb.tree) GtdbTreeR95Bac (class in magna.gtdb.tree) gunc_all_levels_gtdb_r95() (in module magna.gunc) gunc_contig_assignment_gtdb_r95() (in module magna.gunc) gunc_max_css_scores_gtdb_r95() (in module magna.gunc) GuncAllScores (class in magna.gunc) GuncMaxCssScores (class in magna.gunc)

H

Hit (class in magna.hmmer.tophit)

I

is_valid_ncbi_gid() (in module magna.ncbi.accession)

M

magna command line option --install-completion --show-completion magna-ncbi-download command line option --file GID TARGET magna-rq-conda command line option CMD ENV QUEUE

magna-rq-delete command line option QUEUE md5 (magna.gtdb.metadata.GtdbMetadata attribute) (magna.gtdb.tree.GtdbTree attribute) md5sum() (in module magna.util.disk) move_file() (in module magna.util.disk)

O

optimise_df() (in module magna.util.pandas)

P

path (magna.gtdb.metadata.GtdbMetadata attribute) (magna.gtdb.tree.GtdbTree attribute)

PFAM_27 (in module magna.pfam)

Q

QUEUE magna-rq-conda command line option magna-rq-delete command line option

R

R202 (magna.gtdb.enums.GtdbRelease attribute) R207 (magna.gtdb.enums.GtdbRelease attribute) R80 (magna.gtdb.enums.GtdbRelease attribute) R83 (magna.gtdb.enums.GtdbRelease attribute) R86 (magna.gtdb.enums.GtdbRelease attribute) R89 (magna.gtdb.enums.GtdbRelease attribute) R95 (magna.gtdb.enums.GtdbRelease attribute) read_contig_assignments_tsv() (in module magna.gunc) read_diamond_output() (in module magna.diamond)

read_pfam() (in module magna.pfam) read_pfam_tophit() (in module magna.pfam) read_tigrfam() (in module magna.tigrfam) read_tigrfam_tophit() (in module magna.tigrfam) root (magna.gtdb.genome.Genome attribute) rq_delete_queue() (in module magna.rq) rq_enqueue_conda() (in module magna.rq) rq_run_conda() (in module magna.rq) rq_start_worker() (in module magna.rq)

S

source (magna.gtdb.metadata.GtdbMetadata attribute) (magna.gtdb.tree.GtdbTree attribute)

T

TARGET magna-ncbi-download command line option

TIGRFAM_15 (in module magna.tigrfam) TopHitFile (class in magna.hmmer.tophit) tree (magna.gtdb.tree.GtdbTree attribute)

U

untar() (in module magna.util.disk)