Table 4.

Common command line options used throughout the DAWGPAWS suite of programs.

Option	Description
--indir or --infile	For batch scripts, this indicates the input directory containing the FASTA files to annotate. For conversion scripts, this indicates the input file to convert from the native format to the GFF format.
--outdir or --outfile	For batch scripts, this indicates the output directory containing the annotation results for the program and the GFF results. For conversion scripts, this indicates the path to the GFF output file.
--config	For programs that make use of a configuration file, this indicates the path to the configuration file to use.
--seqname	For conversion scripts, this indicates the sequence id to use in the GFF output file.
--param	For conversion scripts, this indicates the name of that parameter set used with the annotation program. This option allows the user to distinguish among multiple parameter sets for the same annotation program, and this parameter name is appended to the source column of the GFF output file.
--program	For conversion scripts, this indicates the name of the program used to generate the annotation result.
--version	Print the current version of the script.
--usage	Print a short program usage message.
--help	Print a short help message including the common usage and all program options available at the command line.
--man	Print the full program manual.
--verbose	This will run the program with maximum verbosity. This option will generate status updates while the program is running, and will maximize the error reporting functions of the script. All verbose statements are written to the standard error output stream.