ncbi¶
Download data from NCBI
Download a set of sequences from NCBI based on a query string ncbi_query and database ncbi_db. This tempate will run only once, after a succesful run it creates a lock file that you need to remove to rerun
Commands¶
- clean
- Remove all job data, not the Moa job itself, note that this must be implemented by the template.
- run
- Download from NCBI
Parameters¶
- db
NCBI database
type: stringdefault: nuccoreoptional: True- query
NCBI query (for example txid9397[Organism%3Aexp])
type: stringdefault: ``optional: False- rename_sequence
try to rename the sequence - note, this does not work if you are downloading more than one sequence
type: booleandefault: Falseoptional: True- sequence_name
Name of the file to write the downloaded sequences to. Use ‘from_dir’ to have the sequence name extracted from the directory name
type: stringdefault: outoptional: True
miscellaneous¶
- Backend
- ruff
- Author
- Mark Fiers
- Creation date
- Wed Nov 10 07:56:48 2010
- Modification date
- Wed Nov 10 07:56:48 2010