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gt-speck - Online in the Cloud

Run gt-speck in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gt-speck 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-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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