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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 <gt-users@genometools.org>.
07/29/2016 GenomeTools 1.5.9