gt-speck - Online in the Cloud

PROGRAM:

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 (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 <[email protected]>.

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