genomepy.providers.ucsc.UcscProvider

class genomepy.providers.ucsc.UcscProvider

Bases: BaseProvider

UCSC genome provider.

The UCSC API REST server is used to search and list genomes. The UCSC MySQL database is used to find metadata and annotations.

__init__()

Methods

`__init__`()
`annotation_links`(name, **kwargs)	Return a sorted list of available gene annotation types for a genome
`assembly_accession`(name)	Return the assembly accession (GCA_/GCF_) for a genome.
`download_annotation`(name[, genomes_dir, ...])	Download the UCSC genePred via their MySQL database, and convert to annotations.
`download_genome`(name[, genomes_dir, ...])	Download a (gzipped) genome file to a specific directory
`genome_taxid`(name)	Return the genome taxonomy ID for a genome.
`get_annotation_download_link`(name, **kwargs)	Return an available annotation type.
`get_annotation_download_links`(name, **kwargs)	Return available gene annotation table(s) from the UCSC MySQL database.
`get_genome_download_link`(name[, mask])	Return UCSC http link to genome sequence
`head_annotation`(name[, genomes_dir, n])	Download the first n genes of each UCSC annotation type.
`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, **kwargs) → List[str]

Return a sorted list of available gene annotation types for a genome

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

assembly_accession(name: str) → str

Return the assembly accession (GCA_/GCF_) for a genome.

Some accession IDs can be retrieved from the UCSC MySQL hgFixed database. For others, the accession IDs can sometimes be scraped from the readme.html. If not, any linked NCBI assembly pages can also be scraped.

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

description_fields = ['description', 'scientificName']: Metadata fields with assembly related info.

download_annotation(name, genomes_dir=None, localname=None, **kwargs): Download the UCSC genePred via their MySQL database, and convert to annotations.

download_genome(name: str, genomes_dir: str = None, localname: str = None, mask: str = 'soft', **kwargs)

Download a (gzipped) genome file to a specific directory

Parameters

name (str) – Genome / species name
genomes_dir (str , optional) – Directory to install genome
localname (str , optional) – Custom name for your genome
mask (str , optional) – Masking, soft, hard or none (all other strings)

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 an available annotation type.

Parameters

name (str) – genome name
**kwargs (dict, optional:) – ucsc_annotation_type : specific annotation type to download.

Returns

http/ftp link

Return type

str

Raises

GenomeDownloadError – if no functional link was found
FileNotFoundError – if the specified annotation type is unavailable

get_annotation_download_links(name, **kwargs)

Return available gene annotation table(s) from the UCSC MySQL database.

Available tables were retrieved on init.

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

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

Return UCSC http link to genome sequence

Parameters

name (str) – Genome name. Current implementation will fail if exact name is not found.
mask (str , optional) – Masking level. Options: soft, hard or none. Default is soft.

Return type

str with the http/ftp download link.

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

Download the first n genes of each UCSC annotation type.

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.
kwargs (dict , optional) –

annotationslist
specify which UCSC annotation types to download. Downloads all available if left blank.

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