annotate
Add or update genome metadata of an index from a CSV file, or dump the current metadata as CSV.
obikmer annotate INDEX --csv FILE [OPTIONS]
obikmer annotate INDEX --dump
Arguments
| Argument |
Description |
INDEX |
Index directory to annotate (modified in place) |
Options
| Option |
Default |
Description |
--csv |
— |
CSV file of metadata to apply (must contain an id column); required unless --dump is used |
--sep |
, |
CSV field separator |
--id-col |
id |
Name of the column containing genome labels |
--na-value |
NA |
Value meaning "remove this field" (deletes the existing key if present) |
--no-overwrite |
off |
Do not overwrite existing metadata keys |
--dump |
off |
Print all genome metadata as CSV to stdout instead of applying a file |