offsets = {
chr1 = 1000,
chr2 = 500
}
NAME
gt-gff3 - Parse, possibly transform, and output GFF3 files.
SYNOPSIS
gt gff3 [option …] [GFF3_file …]
DESCRIPTION
- -sort [yes|no]
-
sort the GFF3 features (memory consumption is proportional to the input file size(s)) (default: no)
- -sortlines [yes|no]
-
sort the GFF3 features on a strict line basis (not sorted asdefined by GenomeTools) (default: no)
- -sortnum [yes|no]
-
enable natural numeric sorting for sequence regions (not sorted as defined by GenomeTools) (default: no)
- -tidy [yes|no]
-
try to tidy the GFF3 files up during parsing (default: no)
- -retainids [yes|no]
-
when available, use the original IDs provided in the source file (memory consumption is proportional to the input file size(s)) (default: no)
- -checkids [yes|no]
-
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 # line the GFF3 parser tries to treat them as a multi-line feature. This requires at least matching sequence IDs and types. (default: no)
- -addids [yes|no]
-
add missing "##sequence-region" lines automatically (default: yes)
- -fixregionboundaries [yes|no]
-
automatically adjust "##sequence-region" lines to contain all their features (memory consumption is proportional to the input file size(s)) (default: no)
- -addintrons [yes|no]
-
add intron features between existing exon features (default: no)
- -offset [value]
-
transform all features by the given offset
- -offsetfile [filename]
-
transform all features by the offsets given in file (default: undefined)
- -setsource [string]
-
set the source value (2nd column) of each feature (default: undefined)
- -typecheck [string]
-
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 .obo is added to the argument and loading the resulting filename from the gtdata/obo_files directory is attempted. (default: undefined)
- -xrfcheck [string]
-
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, .xrf_abbr is added to the argument and loading the resulting filename from the gtdata/xrf_abbr directory is attempted. (default: undefined)
- -show [yes|no]
-
show GFF3 output (default: yes)
- -v [yes|no]
-
be verbose (default: no)
- -width [value]
-
set output width for FASTA sequence printing (0 disables formatting) (default: 0)
- -o [filename]
-
redirect output to specified file (default: undefined)
- -gzip [yes|no]
-
write gzip compressed output file (default: no)
- -bzip2 [yes|no]
-
write bzip2 compressed output file (default: no)
- -force [yes|no]
-
force writing to output file (default: no)
- -help
-
display help and exit
- -version
-
display version information and exit
File format for option -offsetfile:
The file supplied to option -offsetfile defines a mapping table named “offsets”. It maps the sequence-region entries given in the GFF3_file to offsets. It can be defined as follows:
When this example is used, all features with seqid “chr1” will be offset by 1000 and all features with seqid “chr2” by 500.
If -offsetfile is used, offsets for all sequence-regions contained in the given GFF3 files must be defined.
REPORTING BUGS
Report bugs to https://github.com/genometools/genometools/issues.