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This is the command gt-gff3 that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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 <[email protected]>.

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