factory
ensembl.io.genomio.database.factory
¶
Generates one JSON file per metadata type inside manifest
, including the manifest itself.
format_db_data(server_url, dbs, brc_mode=False)
¶
Returns a metadata list from the given databases on a server.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
server_url
|
URL
|
Server URL where all the databases are hosted. |
required |
dbs
|
list[str]
|
List of database names. |
required |
brc_mode
|
bool
|
If true, assign |
False
|
Returns:
Type | Description |
---|---|
list[dict]
|
List of dictionaries with 3 keys: "database", "species" and "division". |
Source code in src/python/ensembl/io/genomio/database/factory.py
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|
get_core_dbs_metadata(server_url, *, prefix='', build=None, version=None, db_regex='', db_list=None, brc_mode=False)
¶
Returns all the metadata fetched for the selected core databases.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
server_url
|
URL
|
Server URL where the core databases are stored. |
required |
prefix
|
str
|
Filter by prefix (no "_" is added automatically). |
''
|
build
|
int | None
|
Filter by VEuPathDB build number. |
None
|
version
|
int | None
|
Filter by Ensembl version. |
None
|
db_regex
|
str
|
Filter by dbname regular expression. |
''
|
db_list
|
Path | None
|
Explicit list of database names. |
None
|
brc_mode
|
bool
|
Enable BRC mode. |
False
|
Returns:
Type | Description |
---|---|
list[dict]
|
List of dictionaries with 3 keys: "database", "species" and "division". |
Source code in src/python/ensembl/io/genomio/database/factory.py
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|
main(arg_list=None)
¶
Main script entry-point.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
arg_list
|
list[str] | None
|
Arguments to parse passing list to parse_args(). |
None
|
Source code in src/python/ensembl/io/genomio/database/factory.py
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|
parse_args(arg_list)
¶
Return a populated namespace with the arguments parsed from a list or from the command line.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
arg_list
|
list[str] | None
|
List of arguments to parse. If |
required |
Source code in src/python/ensembl/io/genomio/database/factory.py
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|