Man page - gt-gff3(1)
Packages contas this manual
- gt-scriptfilter(1)
- gt-mmapandread(1)
- gt-gff3(1)
- gt-ltrdigest(1)
- gt-encseq(1)
- gt-extractfeat(1)
- gt-seed_extend(1)
- gt-dupfeat(1)
- gt-csa(1)
- gt-clean(1)
- gt-packedindex(1)
- gt-genomediff(1)
- gt-sketch_page(1)
- gt-compreads-refcompress(1)
- gt-splicesiteinfo(1)
- gt-extractseq(1)
- gt-compreads(1)
- gt-encseq-decode(1)
- gt-cds(1)
- gt-encseq-bitextract(1)
- gt-readjoiner(1)
- gt-tallymer-occratio(1)
- gt-tallymer(1)
- gt-sequniq(1)
- gt-id_to_md5(1)
- gt-readjoiner-prefilter(1)
- gt-seqtranslate(1)
- gt-tallymer-search(1)
- gt-condenseq(1)
- gt-seqmutate(1)
- gt-seqorder(1)
- gt-seq(1)
- gt-inlineseq_add(1)
- gt-repfind(1)
- gt-seqfilter(1)
- gt-sketch(1)
- gt-hop(1)
- gt-seqids(1)
- gt-fastq_sample(1)
- gt-compreads-refdecompress(1)
- gt-readjoiner-assembly(1)
- gt-readjoiner-overlap(1)
- gt-splitfasta(1)
- gt-seqtransform(1)
- gt-tallymer-mkindex(1)
- gt-wtree(1)
- gt-ltrharvest(1)
- gt-chseqids(1)
- gt-compreads-decompress(1)
- gt-orffinder(1)
- gt-encseq-sample(1)
- gt-encseq-md5(1)
- gt-merge(1)
- gt-gff3validator(1)
- gt-matchtool(1)
- gt-congruence(1)
- gt-tagerator(1)
- gt-gff3_to_gtf(1)
- gt-featureindex(1)
- gt-md5_to_id(1)
- gt-mkfeatureindex(1)
- gt-tirvish(1)
- gt-snpper(1)
- gt-prebwt(1)
- gt-stat(1)
- gt-speck(1)
- gt-convertseq(1)
- gt-compreads-compress(1)
- gt-interfeat(1)
- gt-chain2dim(1)
- gt-encseq-bench(1)
- gt-shulengthdist(1)
- gt-encseq-encode(1)
- gt-select(1)
- gt-uniq(1)
- gt-shredder(1)
- gt-fingerprint(1)
- gt-matstat(1)
- gt-encseq-info(1)
- gt-congruence-spacedseed(1)
- gt-encseq2spm(1)
- gt-simreads(1)
- gt(1)
- gt-dot(1)
- gt-ltrclustering(1)
- gt-seqstat(1)
- gt-mergefeat(1)
- gt-bed_to_gff3(1)
- gt-uniquesub(1)
- gt-gtf_to_gff3(1)
- gt-eval(1)
- gt-encseq-check(1)
- gt-loccheck(1)
- gt-inlineseq_split(1)
Package: genometools
apt-get install genometools
apt-get install genometools
Manuals in package:
Documentations in package:
Manual
| GT-GFF3(1) | GenomeTools Manual | GT-GFF3(1) |
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 https://github.com/genometools/genometools/issues.
| 04/27/2024 | GenomeTools 1.6.5 |