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:

           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.

REPORTING BUGS

       Report bugs to <gt-users@genometools.org>.