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:
offsets = {
chr1 = 1000,
chr2 = 500
}
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.
