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:
-
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.