NAME
gffutils-cli - Command line interface for python-gffutils.
DESCRIPTION
usage: gffutils-cli [-h]
-
{fetch,children,parents,region,create,common,clean,search,sanitize,rmdups} ...
positional arguments:
-
{fetch,children,parents,region,create,common,clean,search,sanitize,rmdups}
- fetch
-
Fetch IDs.
- children
-
Fetch children from the database according to ID.
- parents
-
Fetch parents from the database according to ID.
- region
-
Returns features within provided genomic coordinates.
- create
-
Create a database.
- common
-
Identify child features in common (e.g., common exons across multiple isoforms)
- clean
-
Perform various QC operations to clean a GFF or GTF file.
- search
-
Search the attributes.
- sanitize
-
Sanitize a GFF file. Might get merged with clean feature later. Cleans and adds useful annotations to a GFF file: - Ensures that start > end in all entries - Adds an entry id (eid) to each entry to make files grep-able Outputs result to stdout unless asked to sanitize in place.
- rmdups
-
Remove duplicates from a GFF file.
options:
- -h, --help
-
show this help message and exit