GFFUTILS-CLI

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