Man page - gffutils-cli(1)

Packages contains this manual

Package:  python3-gffutils
apt-get install python3-gffutils

Manuals in package:
• gffutils-cli(1)
• gffutils-cli-clean(1)
• gffutils-cli-sanitize(1)
• gffutils-cli-common(1)
• gffutils-cli-region(1)
• gffutils-cli-create(1)
• gffutils-cli-rmdups(1)
• gffutils-cli-parents(1)
• gffutils-cli-fetch(1)
• gffutils-cli-children(1)
Documentations in package:
• python3-gffutils

Manual

GFFUTILS-CLI

NAME
DESCRIPTION
positional arguments:
options:

---

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

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