Index

C

cache_dir (in module spirepy.data)

cluster_metadata() (in module spirepy.data)

D

download() (in module spirepy.cli) (in module spirepy.cli.download) download_assemblies() (spirepy.Study method) (spirepy.study.Study method) download_genecalls() (spirepy.Study method) (spirepy.study.Study method)

download_mags() (spirepy.Sample method) (spirepy.sample.Sample method) (spirepy.Study method) (spirepy.study.Study method) download_proteins() (spirepy.Study method) (spirepy.study.Study method)

F

formatter (in module spirepy.logger)

G

Genome (class in spirepy.genome) genome_metadata() (in module spirepy.data) get_amr_annotations() (spirepy.Sample method) (spirepy.sample.Sample method) get_contig_depths() (spirepy.Sample method) (spirepy.sample.Sample method) get_eggnog_data() (spirepy.Sample method) (spirepy.sample.Sample method) get_mags() (spirepy.Sample method) (spirepy.sample.Sample method) (spirepy.Study method) (spirepy.study.Study method)

get_metadata() (spirepy.Sample method) (spirepy.sample.Sample method) (spirepy.Study method) (spirepy.study.Study method) get_samples() (spirepy.Study method) (spirepy.study.Study method)

H

handler (in module spirepy.logger)

I

id (spirepy.genome.Genome attribute) (spirepy.Sample attribute) (spirepy.sample.Sample attribute)

is_release (in module spirepy)

L

logger (in module spirepy.logger)

M

main() (in module spirepy.cli) (in module spirepy.cli.spire) maincall() (in module spirepy.cli.spire) memory (in module spirepy.data) module spirepy spirepy.cli spirepy.cli.download spirepy.cli.spire spirepy.cli.view spirepy.data spirepy.genome spirepy.logger spirepy.sample spirepy.study

N

name (spirepy.Study attribute) (spirepy.study.Study attribute)

S

Sample (class in spirepy) (class in spirepy.sample) sample (spirepy.genome.Genome attribute) spirepy module spirepy.cli module spirepy.cli.download module spirepy.cli.spire module spirepy.cli.view module

spirepy.data module spirepy.genome module spirepy.logger module spirepy.sample module spirepy.study module Study (class in spirepy) (class in spirepy.study) study (spirepy.Sample attribute) (spirepy.sample.Sample attribute)

V

view() (in module spirepy.cli) (in module spirepy.cli.view)