Index

_

__init__() (genomepy.annotation.Annotation method) (genomepy.genome.Genome method) (genomepy.plugins.blacklist.BlacklistPlugin method) (genomepy.plugins.bowtie2.Bowtie2Plugin method) (genomepy.plugins.bwa.BwaPlugin method) (genomepy.plugins.gmap.GmapPlugin method) (genomepy.plugins.hisat2.Hisat2Plugin method) (genomepy.plugins.minimap2.Minimap2Plugin method) (genomepy.plugins.Plugin method) (genomepy.plugins.star.StarPlugin method) (genomepy.providers.base.BaseProvider method) (genomepy.providers.ensembl.EnsemblProvider method) (genomepy.providers.gencode.GencodeProvider method) (genomepy.providers.local.LocalProvider method) (genomepy.providers.ncbi.NcbiProvider method) (genomepy.providers.Provider method) (genomepy.providers.ucsc.UcscProvider method) (genomepy.providers.url.UrlProvider method)

A

accession_fields (genomepy.providers.base.BaseProvider attribute) (genomepy.providers.ensembl.EnsemblProvider attribute) (genomepy.providers.gencode.GencodeProvider attribute) (genomepy.providers.local.LocalProvider attribute) (genomepy.providers.ncbi.NcbiProvider attribute) (genomepy.providers.ucsc.UcscProvider attribute) (genomepy.providers.url.UrlProvider attribute) activate() (in module genomepy.plugins) add_accessions1() (in module genomepy.providers.ucsc) add_accessions2() (in module genomepy.providers.ucsc) add_annotation_links() (in module genomepy.providers.ucsc) add_grch37() (in module genomepy.providers.ensembl) (in module genomepy.providers.gencode) Annotation (class in genomepy.annotation) annotation_bed_file (genomepy.annotation.Annotation attribute) (genomepy.genome.Genome attribute) annotation_contigs (genomepy.annotation.Annotation attribute) annotation_gtf_file (genomepy.annotation.Annotation attribute) (genomepy.genome.Genome attribute)

annotation_links() (genomepy.providers.base.BaseProvider method) (genomepy.providers.ensembl.EnsemblProvider method) (genomepy.providers.gencode.GencodeProvider method) (genomepy.providers.local.LocalProvider method) (genomepy.providers.ncbi.NcbiProvider method) (genomepy.providers.ucsc.UcscProvider method) (genomepy.providers.url.UrlProvider method) as_seqdict() (in module genomepy.seq) assembly_accession (genomepy.genome.Genome attribute) assembly_accession() (genomepy.providers.base.BaseProvider method) (genomepy.providers.ensembl.EnsemblProvider method) (genomepy.providers.gencode.GencodeProvider method) (genomepy.providers.local.LocalProvider method) (genomepy.providers.ncbi.NcbiProvider method) (genomepy.providers.ucsc.UcscProvider method) (genomepy.providers.url.UrlProvider method) attributes() (genomepy.annotation.Annotation method)

B

bad_coords() (in module genomepy.genome.sequences) BaseProvider (class in genomepy.providers.base) bed (genomepy.annotation.Annotation attribute) bed_to_seq() (in module genomepy.genome.sequences)

bed_to_seqs() (in module genomepy.genome.sequences) bgzip_and_name() (in module genomepy.files) BlacklistPlugin (class in genomepy.plugins.blacklist) Bowtie2Plugin (class in genomepy.plugins.bowtie2) BwaPlugin (class in genomepy.plugins.bwa)

C

check_ucsc_tools() (in module genomepy.utils) check_url() (in module genomepy.online) clean() (in module genomepy.caching) cleanpath() (in module genomepy.utils) cmd_ok() (in module genomepy.utils)

connect_ftp_link() (in module genomepy.online) convert() (in module genomepy.plugins) count_columns() (in module genomepy.annotation.utils) create() (genomepy.providers.Provider static method) (in module genomepy.providers) custom_options() (in module genomepy.cli)

D

deactivate() (in module genomepy.plugins) description_fields (genomepy.providers.base.BaseProvider attribute) (genomepy.providers.ensembl.EnsemblProvider attribute) (genomepy.providers.gencode.GencodeProvider attribute) (genomepy.providers.local.LocalProvider attribute) (genomepy.providers.ncbi.NcbiProvider attribute) (genomepy.providers.ucsc.UcscProvider attribute) (genomepy.providers.url.UrlProvider attribute) download_annotation() (genomepy.providers.base.BaseProvider method) (genomepy.providers.ensembl.EnsemblProvider method) (genomepy.providers.gencode.GencodeProvider method) (genomepy.providers.local.LocalProvider method) (genomepy.providers.ncbi.NcbiProvider method) (genomepy.providers.ucsc.UcscProvider method) (genomepy.providers.url.UrlProvider method) (in module genomepy.providers.base) (in module genomepy.providers.ucsc)

download_assembly_report() (in module genomepy.providers.ncbi) download_file() (in module genomepy.online) download_genome() (genomepy.providers.base.BaseProvider method) (genomepy.providers.ensembl.EnsemblProvider method) (genomepy.providers.gencode.GencodeProvider method) (genomepy.providers.local.LocalProvider method) (genomepy.providers.ncbi.NcbiProvider method) (genomepy.providers.ucsc.UcscProvider method) (genomepy.providers.url.UrlProvider method) download_head() (in module genomepy.providers.base)

E

EnsemblProvider (class in genomepy.providers.ensembl) extract_archive() (in module genomepy.files) extract_gzip() (in module genomepy.files)

extract_tarball() (in module genomepy.files) extract_zip() (in module genomepy.files) extracted_file() (in module genomepy.files)

F

filter_fasta() (in module genomepy.files) filter_regex() (genomepy.annotation.Annotation method) (in module genomepy.annotation)

from_attributes() (genomepy.annotation.Annotation method) fuzzy_annotation_search() (in module genomepy.providers.url)

G

gaps (genomepy.genome.Genome attribute) gaps_file (genomepy.genome.Genome attribute) GencodeProvider (class in genomepy.providers.gencode) gene_coords() (genomepy.annotation.Annotation method) generate_annot() (in module genomepy.annotation.utils) generate_config() (in module genomepy.config) generate_env() (in module genomepy.functions) generate_fa_sizes() (in module genomepy.genome) generate_gap_bed() (in module genomepy.genome) genes() (genomepy.annotation.Annotation method) Genome (class in genomepy.genome) genome_contigs (genomepy.annotation.Annotation attribute) genome_dir (genomepy.annotation.Annotation attribute) (genomepy.genome.Genome attribute) genome_file (genomepy.annotation.Annotation attribute) (genomepy.genome.Genome attribute) genome_taxid() (genomepy.providers.base.BaseProvider method) (genomepy.providers.ensembl.EnsemblProvider method) (genomepy.providers.gencode.GencodeProvider method) (genomepy.providers.local.LocalProvider method) (genomepy.providers.ncbi.NcbiProvider method) (genomepy.providers.ucsc.UcscProvider method) (genomepy.providers.url.UrlProvider method) GenomeDownloadError genomepy module genomepy.annotation module genomepy.annotation.mygene module genomepy.annotation.sanitize module genomepy.annotation.utils module genomepy.argparse_support module genomepy.caching module genomepy.cli module genomepy.config module genomepy.exceptions module genomepy.files module genomepy.functions module genomepy.genome module genomepy.genome.sequences module genomepy.online module genomepy.plugins module genomepy.plugins.blacklist module genomepy.plugins.bowtie2 module genomepy.plugins.bwa module genomepy.plugins.gmap module genomepy.plugins.hisat2 module genomepy.plugins.minimap2 module genomepy.plugins.star module genomepy.providers module

genomepy.providers.base module genomepy.providers.ensembl module genomepy.providers.gencode module genomepy.providers.local module genomepy.providers.ncbi module genomepy.providers.ucsc module genomepy.providers.url module genomepy.seq module genomepy.utils module genomes (genomepy.providers.base.BaseProvider attribute) (genomepy.providers.ensembl.EnsemblProvider attribute) (genomepy.providers.gencode.GencodeProvider attribute) (genomepy.providers.local.LocalProvider attribute) (genomepy.providers.ncbi.NcbiProvider attribute) (genomepy.providers.ucsc.UcscProvider attribute) (genomepy.providers.url.UrlProvider attribute) genomes_dir (genomepy.genome.Genome attribute) get_active_plugins() (in module genomepy.plugins) get_annotation_download_link() (genomepy.providers.base.BaseProvider method) (genomepy.providers.ensembl.EnsemblProvider method) (genomepy.providers.gencode.GencodeProvider method) (genomepy.providers.local.LocalProvider method) (genomepy.providers.ncbi.NcbiProvider method) (genomepy.providers.ucsc.UcscProvider method) (genomepy.providers.url.UrlProvider method) get_annotation_download_links() (genomepy.providers.base.BaseProvider method) (genomepy.providers.ensembl.EnsemblProvider method) (genomepy.providers.gencode.GencodeProvider method) (genomepy.providers.local.LocalProvider method) (genomepy.providers.ncbi.NcbiProvider method) (genomepy.providers.ucsc.UcscProvider method) (genomepy.providers.url.UrlProvider method) get_division() (genomepy.providers.ensembl.EnsemblProvider method) get_file_info() (in module genomepy.files) get_gencode2ucsc() (in module genomepy.providers.gencode) get_genome_download_link() (genomepy.providers.ensembl.EnsemblProvider method) (genomepy.providers.gencode.GencodeProvider method) (genomepy.providers.ncbi.NcbiProvider method) (genomepy.providers.ucsc.UcscProvider method) get_genome_size() (in module genomepy.providers.ncbi) get_genomename() (in module genomepy.utils) get_genomes() (in module genomepy.providers.ensembl) (in module genomepy.providers.gencode) (in module genomepy.providers.ncbi) (in module genomepy.providers.ucsc) get_genomes_dir() (in module genomepy.utils) get_install_options() (in module genomepy.cli) get_localname() (in module genomepy.utils) get_random_sequences() (genomepy.genome.Genome method) (in module genomepy.genome.sequences) get_release() (genomepy.providers.ensembl.EnsemblProvider method) get_releases() (genomepy.providers.ensembl.EnsemblProvider static method) (in module genomepy.providers.gencode) get_remotename() (in module genomepy.utils) get_seq() (genomepy.genome.Genome method) get_spliced_seq() (genomepy.genome.Genome method) get_track_type() (in module genomepy.genome.sequences) get_version() (genomepy.providers.ensembl.EnsemblProvider method) glob_ext_files() (in module genomepy.files) GmapPlugin (class in genomepy.plugins.gmap) gtf (genomepy.annotation.Annotation attribute) gtf_dict() (genomepy.annotation.Annotation method) gzip_and_name() (in module genomepy.files)

H

head_annotation() (genomepy.providers.base.BaseProvider method) (genomepy.providers.ensembl.EnsemblProvider method) (genomepy.providers.gencode.GencodeProvider method) (genomepy.providers.local.LocalProvider method) (genomepy.providers.ncbi.NcbiProvider method) (genomepy.providers.ucsc.UcscProvider method) (genomepy.providers.url.UrlProvider method)

head_annotations() (in module genomepy.functions) Hisat2Plugin (class in genomepy.plugins.hisat2)

I

index_file (genomepy.annotation.Annotation attribute) (genomepy.genome.Genome attribute)

init_plugins() (in module genomepy.plugins) install_genome() (in module genomepy.functions)

L

lengths() (genomepy.annotation.Annotation method) list() (genomepy.providers.Provider static method) list_available_genomes() (genomepy.providers.base.BaseProvider method) (genomepy.providers.ensembl.EnsemblProvider method) (genomepy.providers.gencode.GencodeProvider method) (genomepy.providers.local.LocalProvider method) (genomepy.providers.ncbi.NcbiProvider method) (genomepy.providers.ucsc.UcscProvider method) (genomepy.providers.url.UrlProvider method) (in module genomepy.functions)

list_installed_genomes() (in module genomepy.functions) list_online_providers() (in module genomepy.providers) list_plugins() (in module genomepy.plugins) list_providers() (in module genomepy.providers) LocalProvider (class in genomepy.providers.local)

M

manage_config() (in module genomepy.config) manage_plugins() (in module genomepy.plugins) map_genes() (genomepy.annotation.Annotation method) map_locations() (genomepy.annotation.Annotation method) (in module genomepy.providers) Minimap2Plugin (class in genomepy.plugins.minimap2) mkdir_p() (in module genomepy.utils) module genomepy genomepy.annotation genomepy.annotation.mygene genomepy.annotation.sanitize genomepy.annotation.utils genomepy.argparse_support genomepy.caching genomepy.cli genomepy.config genomepy.exceptions genomepy.files genomepy.functions genomepy.genome genomepy.genome.sequences genomepy.online genomepy.plugins genomepy.plugins.blacklist genomepy.plugins.bowtie2 genomepy.plugins.bwa genomepy.plugins.gmap genomepy.plugins.hisat2 genomepy.plugins.minimap2 genomepy.plugins.star genomepy.providers genomepy.providers.base genomepy.providers.ensembl genomepy.providers.gencode genomepy.providers.local genomepy.providers.ncbi genomepy.providers.ucsc genomepy.providers.url genomepy.seq genomepy.utils

N

name (genomepy.annotation.Annotation attribute) (genomepy.genome.Genome attribute) (genomepy.providers.base.BaseProvider attribute) (genomepy.providers.ensembl.EnsemblProvider attribute) (genomepy.providers.gencode.GencodeProvider attribute) (genomepy.providers.local.LocalProvider attribute) (genomepy.providers.ncbi.NcbiProvider attribute) (genomepy.providers.ucsc.UcscProvider attribute) (genomepy.providers.url.UrlProvider attribute)

named_gtf (genomepy.annotation.Annotation attribute) NcbiProvider (class in genomepy.providers.ncbi)

O

online() (genomepy.providers.Provider static method)

online_providers() (in module genomepy.providers)

P

parse_file() (in module genomepy.files) parse_genome() (in module genomepy.argparse_support) ping() (genomepy.providers.base.BaseProvider static method) (genomepy.providers.ensembl.EnsemblProvider static method) (genomepy.providers.gencode.GencodeProvider static method) (genomepy.providers.local.LocalProvider static method) (genomepy.providers.ncbi.NcbiProvider static method) (genomepy.providers.ucsc.UcscProvider static method) (genomepy.providers.url.UrlProvider static method)

Plugin (class in genomepy.plugins) plugin (genomepy.genome.Genome property) Provider (class in genomepy.providers)

Q

query_mygene() (in module genomepy.annotation.mygene)

query_ucsc() (in module genomepy.providers.ucsc)

R

read_annot() (in module genomepy.annotation.utils) read_readme() (in module genomepy.files) read_url() (in module genomepy.online) readme_file (genomepy.annotation.Annotation attribute) (genomepy.genome.Genome attribute) region_to_seq() (in module genomepy.genome.sequences)

regions_to_seqs() (in module genomepy.genome.sequences) releases_with_assembly() (genomepy.providers.ensembl.EnsemblProvider method) rename_contigs() (in module genomepy.providers.base) request_json() (in module genomepy.providers.ensembl) retry() (in module genomepy.online) rm_rf() (in module genomepy.utils) run_index_cmd() (in module genomepy.utils)

S

safe() (in module genomepy.utils) sanitize() (genomepy.annotation.Annotation method) scrape_accession() (in module genomepy.providers.ucsc) search() (genomepy.providers.base.BaseProvider method) (genomepy.providers.ensembl.EnsemblProvider method) (genomepy.providers.gencode.GencodeProvider method) (genomepy.providers.local.LocalProvider method) (genomepy.providers.ncbi.NcbiProvider method) (genomepy.providers.ucsc.UcscProvider method) (genomepy.providers.url.UrlProvider method) (in module genomepy.providers)

search_url_for_annotations() (in module genomepy.providers.url) show_plugins() (in module genomepy.plugins) sizes (genomepy.genome.Genome attribute) sizes_file (genomepy.annotation.Annotation attribute) (genomepy.genome.Genome attribute) StarPlugin (class in genomepy.plugins.star)

T

tax_id (genomepy.annotation.Annotation attribute) (genomepy.genome.Genome attribute) taxid_fields (genomepy.providers.base.BaseProvider attribute) (genomepy.providers.ensembl.EnsemblProvider attribute) (genomepy.providers.gencode.GencodeProvider attribute) (genomepy.providers.local.LocalProvider attribute) (genomepy.providers.ncbi.NcbiProvider attribute) (genomepy.providers.ucsc.UcscProvider attribute) (genomepy.providers.url.UrlProvider attribute)

terminal_formatting() (in module genomepy.cli) terminal_header() (in module genomepy.cli) terminal_subheader() (in module genomepy.cli) track2fasta() (genomepy.genome.Genome method) (in module genomepy.genome.sequences) try_except_pass() (in module genomepy.utils)

U

UcscProvider (class in genomepy.providers.ucsc)

update_readme() (in module genomepy.files) UrlProvider (class in genomepy.providers.url)

W

weighted_selection() (in module genomepy.genome.sequences)

write_annot() (in module genomepy.annotation.utils) write_readme() (in module genomepy.files)