emdb
Module dealing with Electron Microscopy Data Bank (EMDB).
fetch(emdb_ids, save_dir, max_parallel_downloads=1, cacher=None)
async
Fetches volume files from the EMDB database.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
emdb_ids
|
Iterable[str]
|
A list of EMDB IDs to fetch. |
required |
save_dir
|
Path
|
The directory to save the downloaded files. |
required |
max_parallel_downloads
|
int
|
The maximum number of parallel downloads. |
1
|
cacher
|
Cacher | None
|
An optional cacher to use for caching downloaded files. |
None
|
Returns:
| Type | Description |
|---|---|
Mapping[str, Path]
|
A mapping of EMDB IDs to their downloaded files. |
read_emdb_ids_from_csv(file)
Reads EMDB IDs from a CSV file.
The CSV file can provide EMDB IDs in the emdb_id column.
If the CSV contains only one column, every value in that column
is treated as an ID, including the first row.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
file
|
Path
|
A path to a file containing the CSV data. |
required |
Returns: A set of EMDB IDs extracted from the CSV file.