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enpi_api.examples.references

Browse available references

Browse available reference databases and their revisions, fetch them all or get only one. Knowledge of available references and their revisions may be required e.g. in order to correctly configure a Sequence Annotation run.

Get all available references

This example showcases how to fetch all available references - the ones created for your organization and the public ones, available to everyone.

from enpi_api.l2.client.enpi_api_client import EnpiApiClient

with EnpiApiClient() as enpi_client:
    """Fetch all the available reference databases. If no private reference databases are
    configured for your organization, then the results will contain only public reference databases."""

    reference_databases = enpi_client.reference_database_api.get_reference_databases()
    print(reference_databases)

Get a single reference

This example showcases how to get a single reference database revision by it's name, species and (optionally) label.

from enpi_api.l2.client.enpi_api_client import EnpiApiClient

with EnpiApiClient() as enpi_client:
    """Fetch all the available reference databases. If no private references were set
    for your organization yet, result set will contain only the public reference databases"""

    reference_name = "Example reference name"
    reference_species = "Homo sapiens"
    reference_revision_label = "Version 1.0"  # Exact version string format depends on a given reference

    # A single reference can be fetched by its name, species and version
    reference_database_revision = enpi_client.reference_database_api.get_revision_by_name(
        name=reference_name,
        species=reference_species,
        label=reference_revision_label,  # A label can be used to fetch a targeted version of a reference
    )

    """A reference can be fetched without `label` provided as well - in such case it will get the
    latest version of the matched reference available.

    newest_revision = enpi_client.reference_database_api.get_revision_by_name(
        name=reference_name,
        species=reference_species,
    )
    """
 1'''
 2# Browse available references
 3
 4Browse available reference databases and their revisions, fetch them all or get only one.
 5Knowledge of available references and their revisions may be required e.g. in order to correctly configure a Sequence Annotation run.
 6
 7##Get all available references
 8
 9This example showcases how to fetch all available references - the ones created for your organization and the public ones, available to everyone.
10```python
11from enpi_api.l2.client.enpi_api_client import EnpiApiClient
12
13with EnpiApiClient() as enpi_client:
14    """Fetch all the available reference databases. If no private reference databases are
15    configured for your organization, then the results will contain only public reference databases."""
16
17    reference_databases = enpi_client.reference_database_api.get_reference_databases()
18    print(reference_databases)
19
20```
21##Get a single reference
22
23This example showcases how to get a single reference database revision by it's name, species and (optionally) label.
24```python
25from enpi_api.l2.client.enpi_api_client import EnpiApiClient
26
27with EnpiApiClient() as enpi_client:
28    """Fetch all the available reference databases. If no private references were set
29    for your organization yet, result set will contain only the public reference databases"""
30
31    reference_name = "Example reference name"
32    reference_species = "Homo sapiens"
33    reference_revision_label = "Version 1.0"  # Exact version string format depends on a given reference
34
35    # A single reference can be fetched by its name, species and version
36    reference_database_revision = enpi_client.reference_database_api.get_revision_by_name(
37        name=reference_name,
38        species=reference_species,
39        label=reference_revision_label,  # A label can be used to fetch a targeted version of a reference
40    )
41
42    """A reference can be fetched without `label` provided as well - in such case it will get the
43    latest version of the matched reference available.
44
45    newest_revision = enpi_client.reference_database_api.get_revision_by_name(
46        name=reference_name,
47        species=reference_species,
48    )
49    """
50
51```
52'''