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

wormbase_parasite.endpoint_groups.sequence

SequenceMixin

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

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

This mixin provides access to the following endpoints:

GET  /sequence/id/:id
POST /sequence/id
GET  /sequence/region/:species/:region
POST /sequence/region/:species

Any arguments listed with a * are required

get_sequence

SequenceMixin.get_sequence(self, id, db_type=None, expand_3prime=None, expand_5prime=None, data_format=None, mask=None, mask_feature=False, multiple_sequences=False, object_type=None, species=None, sequence_type='genomic')

GET sequence/id/:id

Arguments

  • id* (str): A stable ID
  • db_type (str): Default: None
  • expand_3prime (int): Default: None
  • expand_5prime (int): Default: None
  • format (str): Default: None
  • mask (str): Must be one of ['hard', 'soft'] Default: None
  • mask_feature (boolean): Default: False
  • multiple_sequences (boolean): Default: False
  • object_type (str): Default: None
  • species (str): Default: None
  • sequence_type (str): Must be one of ['genomic', 'cds', 'cdna', 'protein'] Default: 'genomic'

Example

client = wormbase_parasite.WormbaseClient()
client.get_sequence('WBGene00221255')

Raises

  • Exception: If an invalid value is provided for format, mask, or sequence_type

Returns

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

See also: https://parasite.wormbase.org/rest/documentation/info/sequence_id

batch_get_sequence

SequenceMixin.batch_get_sequence(self, ids, db_type=None, expand_3prime=None, expand_5prime=None, data_format=None, mask=None, mask_feature=False, object_type=None, species=None, sequence_type='genomic')

POST sequence/id

Arguments

  • ids* (str or list): A string of comma-separated stable IDs, or a list of these IDs
  • db_type (str): Default: None
  • expand_3prime (int): Default: None
  • expand_5prime (int): Default: None
  • data_format (str): Must be one of ['fasta'] Default: None
  • mask (str): Must be one of ['hard', 'soft'] Default: None
  • mask_feature (boolean): Default: False
  • multiple_sequences (boolean): Default: False
  • object_type (str): Default: None
  • species (str): Default: None
  • sequence_type (str): Must be one of ['genomic', 'cds', 'cdna', 'protein'] Default: 'genomic'

Example

client = wormbase_parasite.WormbaseClient()
id_list = ["WBGene00221255", "__VAR(gene_stable_id_2)__"]
client.batch_get_sequence(id_list)

id_string = "WBGene00221255,__VAR(gene_stable_id_2)__"
client.batch_get_sequence(id_string)

Raises

  • Exception: If an invalid value is provided for data_format, mask, or sequence_type`

Returns

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

See also: https://parasite.wormbase.org/rest/documentation/info/sequence_id_post

get_sequence_for_region

SequenceMixin.get_sequence_for_region(self, region, species, coord_system=None, coord_system_version=None, expand_3prime=None, expand_5prime=None, data_format=None, mask=None, mask_feature=False)

GET sequence/region/:species/:region

Arguments

  • region* (str): Query region. A maximum of 10MB is allowed to be requested at any one time
  • species* (str): Species name/alias
  • coord_system (str): Default: None
  • coord_system_version (str): Default: None
  • expand_3prime (int): Default: None
  • expand_5prime (int): Default: None
  • data_format (str): Must be one of ['fasta'] Default: None
  • mask (str): Must be one of ['hard', 'soft'] Default: None
  • mask_feature (boolean): Default: False

Example

client = wormbase_parasite.WormbaseClient()
client.get_sequence_for_region('Bm_v4_Chr2_contig_001:13847151-13862157:1', 'brugia_malayi_prjna10729')

Raises

  • Exception: If an invalid value is provided for data_format, or mask

Returns

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

See also: https://parasite.wormbase.org/rest/documentation/info/sequence_region

batch_get_sequence_for_region

SequenceMixin.batch_get_sequence_for_region(self, species, regions, data_format=None, coord_system=None, coord_system_version=None, expand_3prime=None, expand_5prime=None, mask=None, mask_feature=False)

POST sequence/region/:species

Arguments

  • species* (str): Species name/alias
  • regions* (str or list): A comma-separated string of query regions, or a list of these regions
  • data_format (str): Must be one of ['fasta'] Default: None
  • coord_system (str): Default: None
  • coord_system_version (str): Default: None
  • expand_3prime (int): Default: None
  • expand_5prime (int): Default: None
  • mask (str): Must be one of ['hard', 'soft'] Default: None
  • mask_feature (boolean): Default: False

Example

client = wormbase_parasite.WormbaseClient()
region_list = ["Bm_v4_Chr2_contig_001:13847151-13862157:1", "Bmal_v3_scaffold139:57600..85000"]
client.batch_get_sequence_for_region('brugia_malayi_prjna10729', region_list)

region_string = "Bm_v4_Chr2_contig_001:13847151-13862157:1,Bmal_v3_scaffold139:57600..85000"
client.batch_get_sequence_for_region('brugia_malayi_prjna10729', region_string)

Raises

  • Exception: If an invalid value is provided for data_format, or mask

Returns

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

See also: https://parasite.wormbase.org/rest/documentation/info/sequence_region_post

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