'\" t
.\"     Title: gt-gff3
.\"    Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author]
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 07/22/2020
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.6.1
.\"  Language: English
.\"
.TH "GT\-GFF3" "1" "07/22/2020" "GenomeTools 1\&.6\&.1" "GenomeTools Manual"
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.SH "NAME"
gt-gff3 \- Parse, possibly transform, and output GFF3 files\&.
.SH "SYNOPSIS"
.sp
\fBgt gff3\fR [option \&...] [GFF3_file \&...]
.SH "DESCRIPTION"
.PP
\fB\-sort\fR [\fIyes|no\fR]
.RS 4
sort the GFF3 features (memory consumption is proportional to the input file size(s)) (default: no)
.RE
.PP
\fB\-sortlines\fR [\fIyes|no\fR]
.RS 4
sort the GFF3 features on a strict line basis (not sorted asdefined by GenomeTools) (default: no)
.RE
.PP
\fB\-sortnum\fR [\fIyes|no\fR]
.RS 4
enable natural numeric sorting for sequence regions (not sorted as defined by GenomeTools) (default: no)
.RE
.PP
\fB\-tidy\fR [\fIyes|no\fR]
.RS 4
try to tidy the GFF3 files up during parsing (default: no)
.RE
.PP
\fB\-retainids\fR [\fIyes|no\fR]
.RS 4
when available, use the original IDs provided in the source file (memory consumption is proportional to the input file size(s)) (default: no)
.RE
.PP
\fB\-checkids\fR [\fIyes|no\fR]
.RS 4
make sure the ID attributes are unique within the scope of each GFF3_file, as required by GFF3 specification (memory consumption is proportional to the input file size(s))\&. If features with the same Parent attribute are not separated by a
\fI#\fR
line the GFF3 parser tries to treat them as a multi\-line feature\&. This requires at least matching sequence IDs and types\&. (default: no)
.RE
.PP
\fB\-addids\fR [\fIyes|no\fR]
.RS 4
add missing "##sequence\-region" lines automatically (default: yes)
.RE
.PP
\fB\-fixregionboundaries\fR [\fIyes|no\fR]
.RS 4
automatically adjust "##sequence\-region" lines to contain all their features (memory consumption is proportional to the input file size(s)) (default: no)
.RE
.PP
\fB\-addintrons\fR [\fIyes|no\fR]
.RS 4
add intron features between existing exon features (default: no)
.RE
.PP
\fB\-offset\fR [\fIvalue\fR]
.RS 4
transform all features by the given offset
.RE
.PP
\fB\-offsetfile\fR [\fIfilename\fR]
.RS 4
transform all features by the offsets given in file (default: undefined)
.RE
.PP
\fB\-setsource\fR [\fIstring\fR]
.RS 4
set the
\fIsource\fR
value (2nd column) of each feature (default: undefined)
.RE
.PP
\fB\-typecheck\fR [\fIstring\fR]
.RS 4
use an ontology given in an OBO file to validate parent\-child relationships\&. If no argument is given, the sofa\&.obo file from the gtdata/obo_files directory is used\&. If an argument is given, it is used as an OBO filename\&. In the case that such a file does not exist
\fI\&.obo\fR
is added to the argument and loading the resulting filename from the gtdata/obo_files directory is attempted\&. (default: undefined)
.RE
.PP
\fB\-xrfcheck\fR [\fIstring\fR]
.RS 4
check Dbxref and Ontology_term attributes for correct syntax according to a abbreviation definition file\&. If no argument is given, the GO\&.xrf_abbs file from the gtdata/xrf_abbr directory is used\&. If an argument is given, it is used as an specific filename for an abbreviation file\&. In the case that such a file does not exist,
\fI\&.xrf_abbr\fR
is added to the argument and loading the resulting filename from the gtdata/xrf_abbr directory is attempted\&. (default: undefined)
.RE
.PP
\fB\-show\fR [\fIyes|no\fR]
.RS 4
show GFF3 output (default: yes)
.RE
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (default: no)
.RE
.PP
\fB\-width\fR [\fIvalue\fR]
.RS 4
set output width for FASTA sequence printing (0 disables formatting) (default: 0)
.RE
.PP
\fB\-o\fR [\fIfilename\fR]
.RS 4
redirect output to specified file (default: undefined)
.RE
.PP
\fB\-gzip\fR [\fIyes|no\fR]
.RS 4
write gzip compressed output file (default: no)
.RE
.PP
\fB\-bzip2\fR [\fIyes|no\fR]
.RS 4
write bzip2 compressed output file (default: no)
.RE
.PP
\fB\-force\fR [\fIyes|no\fR]
.RS 4
force writing to output file (default: no)
.RE
.PP
\fB\-help\fR
.RS 4
display help and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.sp
File format for option \fI\-offsetfile\fR:
.sp
The file supplied to option \fI\-offsetfile\fR defines a mapping table named \(lqoffsets\(rq\&. It maps the sequence\-region entries given in the GFF3_file to offsets\&. It can be defined as follows:
.sp
.if n \{\
.RS 4
.\}
.nf
offsets = {
  chr1  = 1000,
  chr2  = 500
}
.fi
.if n \{\
.RE
.\}
.sp
When this example is used, all features with seqid \(lqchr1\(rq will be offset by 1000 and all features with seqid \(lqchr2\(rq by 500\&.
.sp
If \fI\-offsetfile\fR is used, offsets for all sequence\-regions contained in the given GFF3 files must be defined\&.
.SH "REPORTING BUGS"
.sp
Report bugs to https://github\&.com/genometools/genometools/issues\&.