.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH GFFUTILS-CLI "1" "January 2023" "gffutils-cli 0.11.1" "User Commands"
.SH NAME
gffutils-cli \- Command line interface for python-gffutils.
.SH DESCRIPTION
usage: gffutils\-cli [\-h]
.TP
{fetch,children,parents,region,create,common,clean,search,sanitize,rmdups}
\&...
.SS "positional arguments:"
.IP
{fetch,children,parents,region,create,common,clean,search,sanitize,rmdups}
.TP
fetch
Fetch IDs.
.TP
children
Fetch children from the database according to ID.
.TP
parents
Fetch parents from the database according to ID.
.TP
region
Returns features within provided genomic coordinates.
.TP
create
Create a database.
.TP
common
Identify child features in common (e.g., common exons
across multiple isoforms)
.TP
clean
Perform various QC operations to clean a GFF or GTF
file.
.TP
search
Search the attributes.
.TP
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.
.TP
rmdups
Remove duplicates from a GFF file.
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit