database
ensembl.io.genomio.database
¶
Ensembl core database interface module.
CoreServer
¶
Basic interface to a MySQL server with core databases.
Allows to get a filtered list of databases.
Source code in src/python/ensembl/io/genomio/database/core_server.py
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engine = sqlalchemy.create_engine(server_url)
instance-attribute
¶
get_all_core_names()
¶
Query the server and retrieve all database names that look like Ensembl cores.
Source code in src/python/ensembl/io/genomio/database/core_server.py
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get_cores(*, prefix='', build=None, version=None, dbname_re='', db_list=None)
¶
Returns a list of core databases, filtered if requested.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
prefix
|
str
|
Filter by prefix (no "_" is added automatically). |
''
|
build
|
Optional[int]
|
Filter by VEuPathDB build number. |
None
|
version
|
Optional[int]
|
Filter by Ensembl version. |
None
|
dbname_re
|
str
|
Filter by dbname regular expression. |
''
|
db_list
|
Optional[List[str]]
|
Explicit list of database names. |
None
|
Source code in src/python/ensembl/io/genomio/database/core_server.py
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DBConnectionLite
¶
Bases: DBConnection
Extension to get metadata directly from a database, assuming it has a metadata table.
Source code in src/python/ensembl/io/genomio/database/dbconnection_lite.py
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get_meta_value(meta_key)
¶
Returns the first meta_value for a given meta_key.
Source code in src/python/ensembl/io/genomio/database/dbconnection_lite.py
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get_metadata()
¶
Retrieves all metadata from the meta
table in the database.
Returns:
Type | Description |
---|---|
Dict[str, List]
|
A dict of with key meta_key, and value=List of meta_value. |
Source code in src/python/ensembl/io/genomio/database/dbconnection_lite.py
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get_project_release()
¶
Returns the project release number from the database name. Returns empty string if not found.
Source code in src/python/ensembl/io/genomio/database/dbconnection_lite.py
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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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get_meta_values(db_url, meta_keys)
¶
Returns a set of meta values based on set of 1 or more input DB meta_keys.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
db_url
|
URL
|
Target core database URL. |
required |
meta_keys
|
StrPath | list[str]
|
File path with one meta key per line or list of meta keys. |
required |
Source code in src/python/ensembl/io/genomio/database/meta_getter.py
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