genomepy.providers.url.UrlProvider

class genomepy.providers.url.UrlProvider

Bases: BaseProvider

URL genome provider.

Simply download a genome directly through a url.

__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 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 a functional annotation download link.
`get_annotation_download_links`(name, **kwargs)	Retrieve functioning gene annotation download link(s).
`get_genome_download_link`(url[, mask])
`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])	return an empty generator, same as if no genomes were found at the other providers

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 = []: 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)

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 = []: 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 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)

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
**kwargs (dict, optional:) – to_annotation : direct URL to the gene annotation

Returns

http/ftp link

Return type

str

Raises

GenomeDownloadError – if no functional link was found

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

Retrieve functioning gene annotation download link(s).

If provided, check if the annotation url links to a supported file type (gtf/gff3/bed). Else try to find an annotation in the same location as the genome url.

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

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 = 'URL': Name of this provider.

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

search(term, exact=False, size=False): return an empty generator, same as if no genomes were found at the other providers

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