Man page - gt-speck(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-SPECK(1) | GenomeTools Manual | GT-SPECK(1) |
NAME
gt-speck - Checks spec definition compliance in GFF3 input.
SYNOPSIS
gt speck [options] [GFF3_file ...]
DESCRIPTION
-specfile [filename]
file with specification definition (default:
undefined)
-colored [yes|no]
show colored output (default: yes)
-provideindex [yes|no]
provide feature index in specfile namespace (requires
O(n) memory for n input features) (default: no)
-sort [yes|no]
sort input before checking (requires O(n) memory for n
input features) (default: no)
-failhard [yes|no]
stop processing and report runtime errors instead of
recording them in the results (default: no)
-output [string]
output format choose from: [json, text, html, statsonly,
tabular] or give path to output driver (default: text)
-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: so)
-seqfile [filename]
set the sequence file from which to take the sequences
(default: undefined)
-encseq [filename]
set the encoded sequence indexname from which to take the
sequences (default: undefined)
-seqfiles
set the sequence files from which to extract the features
use -- to terminate the list of sequence files
-matchdesc [yes|no]
search the sequence descriptions from the input files for
the desired sequence IDs (in GFF3), reporting the first match (default:
no)
-matchdescstart [yes|no]
exactly match the sequence descriptions from the input
files for the desired sequence IDs (in GFF3) from the beginning to the first
whitespace (default: no)
-usedesc [yes|no]
use sequence descriptions to map the sequence IDs (in
GFF3) to actual sequence entries. If a description contains a sequence range
(e.g., III:1000001..2000000), the first part is used as sequence ID
(III) and the first range position as offset (1000001) (default:
no)
-regionmapping [string]
set file containing sequence-region to sequence file
mapping (default: undefined)
-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)
-v [yes|no]
be verbose (default: no)
-help
display help and exit
-version
display version information and exit
REPORTING BUGS
Report bugs to https://github.com/genometools/genometools/issues.
| 04/27/2024 | GenomeTools 1.6.5 |