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Christopher Anna edited this page Aug 8, 2018 · 2 revisions

wormbase_parasite.endpoint_groups.information

InformationMixin

InformationMixin(self, /, *args, **kwargs)

A mixin with methods for accessing the Information section of the Wormbase ParaSite REST API

This mixin provides access to the following endpoints:

GET /info/assembly/:species
GET /info/assembly/:species/:region_name
GET /info/genomes/:name
GET /info/genomes
GET /info/genomes/assembly/:assembly_id
GET /info/genomes/taxonomy/:taxon_name
GET /info/quality/:genome_name
GET /info/version
GET /info/species

Any arguments listed with a * are required

get_assemblies_for_species

InformationMixin.get_assemblies_for_species(self, species, bands=False)

GET /info/assembly/:species

Arguments

  • species* (str): Species name/alias
  • bands (boolean): Default: False

Example

client = wormbase_parasite.WormbaseClient()
client.get_assemblies_for_species('brugia_malayi_prjna10729')

Returns

data (dict): a dictionary representing the data returned by the API

See also: http://parasite.wormbase.org/rest/documentation/info/assembly_info

get_info_for_region

InformationMixin.get_info_for_region(self, region_name, species, bands=False)

GET /info/assembly/:species/:region_name

Arguments

  • region_name* (str): The (top level) sequence region name
  • species* (str): Species name/alias
  • bands (boolean): Default: False

Example

client = wormbase_parasite.WormbaseClient()
client.get_info_for_region('Bm_v4_Chr2_contig_001', 'brugia_malayi_prjna10729')

Returns

data (dict): a dictionary representing the data returned by the API

See also: https://parasite.wormbase.org/rest-10/documentation/info/assembly_stats

get_info_for_genome

InformationMixin.get_info_for_genome(self, genome_name, expand=False)

GET /info/genomes/:name

Arguments

  • name* (str): The production name of the genome
  • expand (boolean): Default: False

Example

client = wormbase_parasite.WormbaseClient()
client.get_info_for_genome('brugia_malayi_prjna10729')

Returns

data (dict): a dictionary representing the data returned by the API

See also: https://parasite.wormbase.org/rest-10/documentation/info/info_genome

get_info_for_all_genomes

InformationMixin.get_info_for_all_genomes(self, expand=False)

GET /info/genomes

Arguments

  • expand (boolean): Default: False Warning Setting this value to True can dramatically increase this function's runtime!

Example

client = wormbase_parasite.WormbaseClient()
client.get_info_for_all_genomes()

Returns

data (list): a list of dictionaries representing the data returned by the API

See also: https://parasite.wormbase.org/rest-10/documentation/info/info_genomes

get_info_for_genome_with_assembly

InformationMixin.get_info_for_genome_with_assembly(self, assembly_id, expand=False)

GET /info/genomes/assembly/:assembly_id

Arguments

  • expand (boolean): Default: False Warning Setting this value to True can dramatically increase this function's runtime!

Example

client = wormbase_parasite.WormbaseClient()
client.get_info_for_genome_with_assembly('GCA_000951595.1')

Returns

data (dict): a dictionary representing the data returned by the API

See also: https://parasite.wormbase.org/rest-10/documentation/info/info_genomes_assembly

get_info_for_taxonomy_node

InformationMixin.get_info_for_taxonomy_node(self, taxon_name, expand=False)

GET /info/genomes/taxonomy/:taxon_name

Arguments

  • taxon_name* (str): Taxon name or NCBI taxonomy ID
  • expand (boolean): Default: False Warning Setting this value to True can dramatically increase this function's runtime!

Example

client = wormbase_parasite.WormbaseClient()
client.get_info_for_taxonomy_node('Brugia')

Returns

data (list): a list of dictionaries representing the data returned by the API

See also: https://parasite.wormbase.org/rest-10/documentation/info/info_genomes_taxonomy

get_quality_scores_for_genome

InformationMixin.get_quality_scores_for_genome(self, genome_name)

GET /info/quality/:genome_name

Arguments

  • genome_name* (str): The production name of the genome

Example

client = wormbase_parasite.WormbaseClient()
client.get_quality_scores_for_genome('brugia_malayi_prjna10729')

Returns

data (dict): a dictionary representing the data returned by the API

See also: https://parasite.wormbase.org/rest-10/documentation/info/info_quality_name

get_release_info

InformationMixin.get_release_info(self)

GET /info/version

This function takes no arguments, but its response is determined by the API version number specified during initialization of the WormbaseClient object.

Example

client = wormbase_parasite.WormbaseClient()
client.get_release_info()

Returns

data (dict): a dictionary representing the data returned by the API

See also: https://parasite.wormbase.org/rest-10/documentation/info/info_wormbase_version

get_available_species

InformationMixin.get_available_species(self)

GET /info/species

Example

client = wormbase_parasite.WormbaseClient()
client.get_available_species()

Returns

data (dict): a dictionary representing the data returned by the API

See also: https://parasite.wormbase.org/rest-10/documentation/info/species

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