Index

A

all_combinations_of_ensembl_genomes() (in module pyensembl.shell)

all_registered_latin_names() (pyensembl.species.Species class method) all_species_release_pairs() (pyensembl.species.Species class method)

C

cache_directory_path (pyensembl.download_cache.DownloadCache attribute) (pyensembl.DownloadCache attribute) cache_subdirectory() (in module pyensembl.download_cache) cached() (pyensembl.ensembl_release.EnsemblRelease class method) (pyensembl.EnsemblRelease class method) cached_dataframe() (pyensembl.memory_cache.MemoryCache method) (pyensembl.MemoryCache method) cached_object() (pyensembl.memory_cache.MemoryCache method) (pyensembl.MemoryCache method) cached_path() (pyensembl.download_cache.DownloadCache method) (pyensembl.DownloadCache method) cached_release() (in module pyensembl) (in module pyensembl.ensembl_release) can_overlap() (pyensembl.Locus method) (pyensembl.locus.Locus method) check_release_number() (in module pyensembl.ensembl_release_versions) check_species_object() (in module pyensembl) (in module pyensembl.species) clear_cache() (pyensembl.Genome method) (pyensembl.SequenceData method) (pyensembl.genome.Genome method) (pyensembl.sequence_data.SequenceData method) clear_cached_objects() (pyensembl.memory_cache.MemoryCache method) (pyensembl.MemoryCache method) coding_sequence (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) coding_sequence_position_ranges (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute)

collect_all_installed_ensembl_releases() (in module pyensembl.shell) collect_selected_genomes() (in module pyensembl.shell) column_exists() (pyensembl.Database method) (pyensembl.database.Database method) column_values_at_locus() (pyensembl.Database method) (pyensembl.database.Database method) columns() (pyensembl.Database method) (pyensembl.database.Database method) complete (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) connect_or_create() (pyensembl.Database method) (pyensembl.database.Database method) connection (pyensembl.Database attribute) (pyensembl.database.Database attribute) contains() (pyensembl.Locus method) (pyensembl.locus.Locus method) contains_locus() (pyensembl.Locus method) (pyensembl.locus.Locus method) contains_start_codon (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) contains_stop_codon (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) contigs() (pyensembl.Genome method) (pyensembl.genome.Genome method) create() (pyensembl.Database method) (pyensembl.database.Database method)

D

Database (class in pyensembl) (class in pyensembl.database) db (pyensembl.Genome attribute) (pyensembl.genome.Genome attribute) delete_cache_directory() (pyensembl.download_cache.DownloadCache method) (pyensembl.DownloadCache method) delete_cached_files() (pyensembl.download_cache.DownloadCache method) (pyensembl.DownloadCache method) delete_file() (pyensembl.memory_cache.MemoryCache method) (pyensembl.MemoryCache method) delete_index_files() (pyensembl.Genome method) (pyensembl.genome.Genome method)

distance_to_interval() (pyensembl.Locus method) (pyensembl.locus.Locus method) distance_to_locus() (pyensembl.Locus method) (pyensembl.locus.Locus method) distinct_column_values_at_locus() (pyensembl.Database method) (pyensembl.database.Database method) download() (pyensembl.Genome method) (pyensembl.genome.Genome method) download_or_copy_if_necessary() (pyensembl.download_cache.DownloadCache method) (pyensembl.DownloadCache method) DownloadCache (class in pyensembl) (class in pyensembl.download_cache) dump_pickle() (in module pyensembl.common)

E

EnsemblRelease (class in pyensembl) (class in pyensembl.ensembl_release) Exon (class in pyensembl), [1] (class in pyensembl.exon) exon_by_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) exon_ids() (pyensembl.Genome method) (pyensembl.genome.Genome method) exon_ids_at_locus() (pyensembl.Genome method) (pyensembl.genome.Genome method) exon_ids_of_gene_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) exon_ids_of_gene_name() (pyensembl.Genome method) (pyensembl.genome.Genome method)

exon_ids_of_transcript_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) exon_ids_of_transcript_name() (pyensembl.Genome method) (pyensembl.genome.Genome method) exon_intervals (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) exons (pyensembl.Gene attribute) (pyensembl.Transcript attribute) (pyensembl.gene.Gene attribute) (pyensembl.transcript.Transcript attribute) exons() (pyensembl.Genome method) (pyensembl.genome.Genome method) exons_at_locus() (pyensembl.Genome method) (pyensembl.genome.Genome method)

F

fasta_dictionary (pyensembl.sequence_data.SequenceData attribute) (pyensembl.SequenceData attribute) find_nearest_locus() (in module pyensembl) (in module pyensembl.search) find_species_by_name() (in module pyensembl) (in module pyensembl.species) find_species_by_reference() (in module pyensembl)

first_start_codon_spliced_offset (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) five_prime_utr_sequence (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) from_dict() (pyensembl.ensembl_release.EnsemblRelease class method) (pyensembl.EnsemblRelease class method) (pyensembl.species.Species class method)

G

Gene (class in pyensembl) (class in pyensembl.gene) gene (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) gene_by_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) gene_by_protein_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) gene_id_of_protein_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) gene_ids() (pyensembl.Genome method) (pyensembl.genome.Genome method) gene_ids_at_locus() (pyensembl.Genome method) (pyensembl.genome.Genome method) gene_ids_of_gene_name() (pyensembl.Genome method) (pyensembl.genome.Genome method) gene_name (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) gene_name_of_exon_id() (pyensembl.Genome method) (pyensembl.genome.Genome method)

gene_name_of_gene_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) gene_name_of_transcript_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) gene_name_of_transcript_name() (pyensembl.Genome method) (pyensembl.genome.Genome method) gene_names() (pyensembl.Genome method) (pyensembl.genome.Genome method) gene_names_at_locus() (pyensembl.Genome method) (pyensembl.genome.Genome method) genes() (pyensembl.Genome method) (pyensembl.genome.Genome method) genes_at_locus() (pyensembl.Genome method) (pyensembl.genome.Genome method) genes_by_name() (pyensembl.Genome method) (pyensembl.genome.Genome method) Genome (class in pyensembl) (class in pyensembl.genome) genome_for_reference_name() (in module pyensembl) get() (pyensembl.sequence_data.SequenceData method) (pyensembl.SequenceData method)

I

id (pyensembl.Exon attribute), [1] (pyensembl.Gene attribute) (pyensembl.Transcript attribute) (pyensembl.exon.Exon attribute) (pyensembl.gene.Gene attribute) (pyensembl.transcript.Transcript attribute) index() (pyensembl.Genome method) (pyensembl.SequenceData method) (pyensembl.genome.Genome method) (pyensembl.sequence_data.SequenceData method)

install_string() (pyensembl.ensembl_release.EnsemblRelease method) (pyensembl.EnsemblRelease method) (pyensembl.Genome method) (pyensembl.genome.Genome method) is_empty() (pyensembl.memory_cache.MemoryCache method) (pyensembl.MemoryCache method) is_url_format() (pyensembl.download_cache.DownloadCache method) (pyensembl.DownloadCache method)

L

last_stop_codon_spliced_offset (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) length (pyensembl.Locus attribute) (pyensembl.locus.Locus attribute) load_pickle() (in module pyensembl.common) local_db_filename (pyensembl.Database attribute) (pyensembl.database.Database attribute) local_db_path (pyensembl.Database attribute) (pyensembl.database.Database attribute) local_path_or_install_error() (pyensembl.download_cache.DownloadCache method) (pyensembl.DownloadCache method)

loci_of_gene_names() (pyensembl.Genome method) (pyensembl.genome.Genome method) Locus (class in pyensembl) (class in pyensembl.locus) locus_of_exon_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) locus_of_gene_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) locus_of_transcript_id() (pyensembl.Genome method) (pyensembl.genome.Genome method)

M

make_fasta_filename() (in module pyensembl.ensembl_url_templates) make_fasta_url() (in module pyensembl.ensembl_url_templates) make_gtf_filename() (in module pyensembl.ensembl_url_templates) make_gtf_url() (in module pyensembl.ensembl_url_templates)

memoize() (in module pyensembl.common) MemoryCache (class in pyensembl) (class in pyensembl.memory_cache) MissingLocalFile MissingRemoteFile

N

name (pyensembl.Gene attribute) (pyensembl.Transcript attribute) (pyensembl.gene.Gene attribute) (pyensembl.transcript.Transcript attribute) normalize_init_values() (pyensembl.ensembl_release.EnsemblRelease class method) (pyensembl.EnsemblRelease class method)

normalize_reference_name() (in module pyensembl) normalize_release_properties() (in module pyensembl.ensembl_url_templates) normalize_species_name() (in module pyensembl) (in module pyensembl.species)

O

offset() (pyensembl.Locus method) (pyensembl.locus.Locus method) offset_range() (pyensembl.Locus method) (pyensembl.locus.Locus method) on_backward_strand (pyensembl.Locus attribute) (pyensembl.locus.Locus attribute) on_contig() (pyensembl.Locus method) (pyensembl.locus.Locus method) on_forward_strand (pyensembl.Locus attribute) (pyensembl.locus.Locus attribute)

on_negative_strand (pyensembl.Locus attribute) (pyensembl.locus.Locus attribute) on_positive_strand (pyensembl.Locus attribute) (pyensembl.locus.Locus attribute) on_strand() (pyensembl.Locus method) (pyensembl.locus.Locus method) overlaps() (pyensembl.Locus method) (pyensembl.locus.Locus method) overlaps_locus() (pyensembl.Locus method) (pyensembl.locus.Locus method)

P

PRIMARY_KEY_COLUMNS (pyensembl.Database attribute) (pyensembl.database.Database attribute) protein_id (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) protein_ids() (pyensembl.Genome method) (pyensembl.genome.Genome method) protein_ids_at_locus() (pyensembl.Genome method) (pyensembl.genome.Genome method) protein_sequence (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) protein_sequence() (pyensembl.Genome method) (pyensembl.genome.Genome method) protein_sequences (pyensembl.Genome attribute) (pyensembl.genome.Genome attribute) pyensembl (module)

pyensembl.common (module) pyensembl.database (module) pyensembl.download_cache (module) pyensembl.ensembl_release (module) pyensembl.ensembl_release_versions (module) pyensembl.ensembl_url_templates (module) pyensembl.exon (module) pyensembl.gene (module) pyensembl.genome (module) pyensembl.locus (module) pyensembl.memory_cache (module) pyensembl.search (module) pyensembl.sequence_data (module) pyensembl.shell (module) pyensembl.species (module) pyensembl.transcript (module)

Q

query() (pyensembl.Database method) (pyensembl.database.Database method) query_distinct_on_contig() (pyensembl.Database method) (pyensembl.database.Database method) query_feature_values() (pyensembl.Database method) (pyensembl.database.Database method)

query_loci() (pyensembl.Database method) (pyensembl.database.Database method) query_locus() (pyensembl.Database method) (pyensembl.database.Database method) query_one() (pyensembl.Database method) (pyensembl.database.Database method)

R

register() (pyensembl.species.Species class method) remove_from_cache() (pyensembl.memory_cache.MemoryCache method) (pyensembl.MemoryCache method) required_local_files() (pyensembl.Genome method) (pyensembl.genome.Genome method) required_local_files_exist() (pyensembl.Genome method) (pyensembl.genome.Genome method) requires_gtf (pyensembl.Genome attribute) (pyensembl.genome.Genome attribute)

requires_protein_fasta (pyensembl.Genome attribute) (pyensembl.genome.Genome attribute) requires_transcript_fasta (pyensembl.Genome attribute) (pyensembl.genome.Genome attribute) run() (in module pyensembl.shell) run_sql_query() (pyensembl.Database method) (pyensembl.database.Database method)

S

sequence (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) SequenceData (class in pyensembl) (class in pyensembl.sequence_data) Species (class in pyensembl.species) spliced_offset() (pyensembl.Transcript method) (pyensembl.transcript.Transcript method) start_codon_positions (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute)

start_codon_spliced_offsets (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) start_codon_unspliced_offsets (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) stop_codon_positions (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) stop_codon_spliced_offsets (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) stop_codon_unspliced_offsets (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute)

T

three_prime_utr_sequence (pyensembl.Transcript attribute) (pyensembl.transcript.Transcript attribute) to_dict() (pyensembl.ensembl_release.EnsemblRelease method) (pyensembl.EnsemblRelease method) (pyensembl.Exon method), [1] (pyensembl.Gene method) (pyensembl.Genome method) (pyensembl.Locus method) (pyensembl.Transcript method) (pyensembl.exon.Exon method) (pyensembl.gene.Gene method) (pyensembl.genome.Genome method) (pyensembl.locus.Locus method) (pyensembl.species.Species method) (pyensembl.transcript.Transcript method) to_tuple() (pyensembl.Locus method) (pyensembl.locus.Locus method) Transcript (class in pyensembl) (class in pyensembl.transcript) transcript_by_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) transcript_by_protein_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) transcript_id_of_protein_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) transcript_ids() (pyensembl.Genome method) (pyensembl.genome.Genome method) transcript_ids_at_locus() (pyensembl.Genome method) (pyensembl.genome.Genome method)

transcript_ids_of_exon_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) transcript_ids_of_gene_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) transcript_ids_of_gene_name() (pyensembl.Genome method) (pyensembl.genome.Genome method) transcript_ids_of_transcript_name() (pyensembl.Genome method) (pyensembl.genome.Genome method) transcript_name_of_transcript_id() (pyensembl.Genome method) (pyensembl.genome.Genome method) transcript_names() (pyensembl.Genome method) (pyensembl.genome.Genome method) transcript_names_at_locus() (pyensembl.Genome method) (pyensembl.genome.Genome method) transcript_names_of_gene_name() (pyensembl.Genome method) (pyensembl.genome.Genome method) transcript_sequence() (pyensembl.Genome method) (pyensembl.genome.Genome method) transcript_sequences (pyensembl.Genome attribute) (pyensembl.genome.Genome attribute) transcripts (pyensembl.Gene attribute) (pyensembl.gene.Gene attribute) transcripts() (pyensembl.Genome method) (pyensembl.genome.Genome method) transcripts_at_locus() (pyensembl.Genome method) (pyensembl.genome.Genome method) transcripts_by_name() (pyensembl.Genome method) (pyensembl.genome.Genome method)

W

which_reference() (in module pyensembl) (pyensembl.species.Species method)