pyensembl 0.5.0

Python interface to ensembl reference genome metadata

pyensembl

Python interface to Ensembl reference genome metadata (exons, transcripts, &c)

from pyensembl import EnsemblRelease

# release 77 uses human reference genome GRCh38
data = EnsemblRelease(77)

# will return ['HLA-A']
gene_names = data.gene_names_at_locus(contig=6, position=29945884)

# get all exons associated with HLA-A
exon_ids  = data.exon_ids_of_gene_name('HLA-A')

API

The EnsemblRelease object has methods to let you access all possible combinations of the annotation features gene_name, gene_id, transcript_name, transcript_id, exon_id as well as the location of these genomic elements (contig, start position, end position, strand).

Gene Names

gene_names() : returns all gene names in the annotation database

gene_names_on_contig(contig) : all gene names on a particular chromosome/contig

gene_names_at_locus(contig, position) : names of genes overlapping with the given locus (returns a list to account for overlapping genes)

gene_names_at_loci(contig, start, end) : names of genes overlapping with the given range of loci

gene_name_of_gene_id(gene_id) : name of gene with given ID

gene_name_of_transcript_id(transcript_id) : name of gene associated with given transcript ID

gene_name_of_transcript_name(transcript_name) : name of gene associated with given transcript name

gene_name_of_exon_id(exon_id) : name of gene associated with given exon ID

Gene IDs

gene_ids() : all gene IDs in the annotation database

gene_ids_on_contig(contig) : all gene IDs on a particular chromosome/contig

gene_id_of_gene_name(gene_name) : translate Ensembl gene ID to its corresponding name

Transcript Names

transcript_names() : all transcript names in the annotation database

transcript_names_on_contig(contig) : all transcript names on a particular chromosome/contig

Transcript IDs

transcript_ids() : returns all transcript IDs in the annotation database

transcript_ids_of_gene_id(gene_id) : return IDs of all transcripts associated with given gene ID

transcript_ids_of_gene_name(gene_name) : return IDs of all transcripts associated with given gene name

transcript_id_of_transcript_name(transcript_name) : translate transcript name to its ID

transcript_ids_of_exon_id(exon_id) : return IDs of all transcripts associatd with given exon ID

Exon IDs

exon_ids() : returns all transcript IDs in the annotation database

exon_ids_of_gene_id

exon_ids_of_gene_name

exon_ids_of_transcript_name

exon_ids_of_transcript_id

Locations

These functions currently assume that each gene maps to a single unique location, which is invalid both with heavily copied genes (e.g. U1) and with polymorphic regions (e.g. HLA genes).

location_of_gene_name(gene_name)

location_of_gene_id(gene_id)

location_of_transcript_id(transcript_id)

location_of_exon_id(exon_id)

Start Codons

start_codon_of_transcript_id

start_codon_of_transcript_name

Stop Codons

stop_codon_of_transcript_id

stop_codon_of_transcript_name