genomepy.providers.gencode.GencodeProvider

class genomepy.providers.gencode.GencodeProvider

Bases: BaseProvider

GENCODE genome provider.

GENCODE sports superb annotations for human and mouse with UCSC-style chromosome names. Genomes on this provider are unmasked, so we use the UCSC genomes instead.

Note: this combination lacks scaffolds and alternate haplotype sequences (their names don’t match between GENCODE and UCSC).

__init__()

Methods

`__init__`()
`annotation_links`(name, **kwargs)	Return available gene annotation links (http/ftp) for a genome
`assembly_accession`(name)	Return the assembly accession number (GCA* or GCF*) for a genome.
`download_annotation`(name[, genomes_dir, ...])	Download annotation file to to a specific directory
`download_genome`(name[, genomes_dir, ...])	Download genomes from UCSC, as the GENCODE genomes aren't masked.
`genome_taxid`(name)	Return the genome taxonomy ID for a genome.
`get_annotation_download_link`(name, **kwargs)	Return a functional annotation download link.
`get_annotation_download_links`(name, **kwargs)	Retrieve functioning gene annotation download link(s).
`get_genome_download_link`(name[, mask])	Return UCSC http link to genome sequence
`head_annotation`(name[, genomes_dir, n])	Download the first n lines of the annotation.
`list_available_genomes`([size])	List all available genomes.
`ping`()	Can the provider be reached?
`search`(term[, exact, size])	Search for term in genome names and descriptions (if term contains text.

Attributes

`accession_fields`	Metadata fields that (can) contain the assembly's accession ID.
`description_fields`	Metadata fields with assembly related info.
`genomes`	Dictionary with assembly names as key and assembly metadata dictionary as value.
`name`	Name of this provider.
`taxid_fields`	Metadata fields that (can) contain the assembly's taxonomy ID.

accession_fields = ['assembly_accession']: Metadata fields that (can) contain the assembly’s accession ID.

annotation_links(name: str, **kwargs) → List[str]

Return available gene annotation links (http/ftp) for a genome

Parameters: name (str) – genome name
Returns: Gene annotation links
Return type: list

assembly_accession(name: str) → str

Return the assembly accession number (GCA* or GCF*) for a genome.

Parameters: name (str) – genome name
Returns: Assembly accession number
Return type: str

description_fields = ['species', 'other_info', 'text_search']: Metadata fields with assembly related info.

download_annotation(name, genomes_dir=None, localname=None, **kwargs)

Download annotation file to to a specific directory

Parameters

name (str) – Genome / species name
genomes_dir (str , optional) – Directory to install annotation
localname (str , optional) – Custom name for your genome

download_genome(name: str, genomes_dir: str = None, localname: str = None, mask: str = 'soft', **kwargs): Download genomes from UCSC, as the GENCODE genomes aren’t masked. Contigs between the UCSC genome and GENCODE annotations match.

genome_taxid(name: str) → int

Return the genome taxonomy ID for a genome.

Parameters: name (str) – genome name
Returns: Genome Taxonomy identifier
Return type: int

genomes = {}: Dictionary with assembly names as key and assembly metadata dictionary as value.

get_annotation_download_link(name: str, **kwargs) → str

Return a functional annotation download link.

Parameters: name (str) – genome name
Returns: http/ftp link
Return type: str
Raises: GenomeDownloadError – if no functional link was found

get_annotation_download_links(name, **kwargs)

Retrieve functioning gene annotation download link(s).

Parameters: name (str) – genome name
Returns: http/ftp link(s)
Return type: list

get_genome_download_link(name: str, mask: str = 'soft', **kwargs) → str

Return UCSC http link to genome sequence

Parameters

name (str) – Genome name.
mask (str , optional) – Masking level. Options: soft, hard or none. Default is soft.

Returns

http/ftp link tp genome.

Return type

str

head_annotation(name: str, genomes_dir=None, n: int = 5, **kwargs)

Download the first n lines of the annotation.

The first line of the GTF is printed for review (of the gene_name field, for instance).

Parameters

name (str) – genome name
genomes_dir (str, optional) – genomes directory to install the annotation in.
n (int, optional) – download the annotation for n genes.

list_available_genomes(size=False)

List all available genomes.

Parameters: size (bool, optional) – Show absolute genome size.
Yields: genomes (list of tuples) – tuples with assembly name, accession, scientific_name, taxonomy id and description

name = 'GENCODE': Name of this provider.

static ping(): Can the provider be reached?

search(term: str, exact=False, size=False)

Search for term in genome names and descriptions (if term contains text. Case-insensitive), assembly accession IDs (if term starts with GCA_ or GCF_), or taxonomy IDs (if term is a number).

Note: exact accession ID search on UCSC may return different patch levels.

Parameters

term (str, int) – Search term, case-insensitive. Can be an assembly name (e.g. hg38), scientific name (Danio rerio), assembly accession ID (GCA_000146045), or taxonomy ID (7227).
exact (bool, optional) – term must be an exact match
size (bool, optional) – Show absolute genome size.

Yields

tuples with name and metadata

taxid_fields = ['taxonomy_id']: Metadata fields that (can) contain the assembly’s taxonomy ID.