GT-GFF3(1)

NAME
gt-gff3 - Parse, possibly transform, and output GFF3 files.

SYNOPSIS

gt gff3 [option ...] [GFF3_file ...]

OPTIONS

-sort
    sort the GFF3 features (memory consumption is proportional to the input file size(s)) (default: no)

-tidy
    try to tidy the GFF3 files up during parsing (default: no)

-retainids
    when available, use the original IDs provided in the source file (memory consumption is proportional to the input file size(s)) (default: no)

-checkids
    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)) (default: no)

-addids
    add missing "##sequence-region" lines automatically (default: yes)

-fixregionboundaries
    automatically adjust "##sequence-region" lines to contain all their features (memory consumption is proportional to the input file size(s)) (default: no)

-addintrons
    add intron features between existing exon features (default: no)

-offset
    transform all features by the given offset (default: undefined)

-offsetfile
    transform all features by the offsets given in file (default: undefined)

-typecheck
    check GFF3 types against "id" and "name" tags in given OBO file (default: undefined)

-show
    show GFF3 output (default: yes)

-v
    be verbose (default: no)

-width
    set output width for FASTA sequence printing (0 disables formatting) (default: 0)

-o
    redirect output to specified file (default: undefined)

-gzip
    write gzip compressed output file (default: no)

-bzip2
    write bzip2 compressed output file (default: no)

-force
    force writing to output file (default: no)

-help
    display help and exit

-version
    display version information and exit

DESCRIPTION

File format for option -offsetfile:

The file supplied to option -offsetfile defines a mapping table named “offsets”. It maps the sequence-regions 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.

AUTHOR

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