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: string
default: nuccore
optional: True
query

NCBI query (for example txid9397[Organism%3Aexp])

type: string
default: ``
optional: False
rename_sequence

try to rename the sequence - note, this does not work if you are downloading more than one sequence

type: boolean
default: False
optional: 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: string
default: out
optional: 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