| cnv_repseek2gff.pl |
cnv_repseek2gff.pl - Convert repseek output to gff format
This documentation refers to program version $Rev: 597 $
cnv_repseek2gff.pl -i InFile -o OutFile
--infile # Path to the repseek output file
# Assumes STDIN if not givien
--outfile # Path to the output gff file
# Assumes STDOUT if not given
Convert repseek output to a GFF format compatible with the Apollo genome annotation program.
Path of the input file. If an input file is not provided, the program will expect input from STDIN.
Path of the output file. If an output path is not provided, the program will write output to STDOUT.
The name of the sequence contig that is being annotated. This will be used for the first column in the gff file. If this option is not specified the name will default to 'seq'.
The name of the parameter set used in repseek. This allows the user to define multiple parameter sets in repseek, and then draw them as separate tracks in annotation visualization programs.
Short overview of how to use program from command line.
Show program usage with summary of options.
Show program version.
Show the full program manual. This uses the perldoc command to print the POD documentation for the program.
Run the program with minimal output.
Run the program in verbose mode.
The input file path provided by the -i, --infile switch is not valid.
The output file path provided by the -o, --outfile witch is not valid.
When an input file path is not specified, the program expects input to come from STDIN. This default behaviour allows output from repseek to be piped directly into the cnv_repseek2gff.pl program.
This program does not make use of configuration files or variables set in the user environment.
This program is designed to parse output from the RepSeek program. RepSeek is available from: http://wwwabi.snv.jussieu.fr/~public/RepSeek/
If you find a bug with this software, file a bug report on the DAWG-PAWS Sourceforge website: http://sourceforge.net/tracker/?group_id=204962
This program has been tested and know to work with RepSeek version 10May2007. Other versions have not been tested for compatibility.
A manuscript is being submitted describing the DAWGPAWS program. Until this manuscript is published, please refer to the DAWGPAWS SourceForge website when describing your use of this program:
JC Estill and JL Bennetzen. 2009. The DAWGPAWS Pipeline for the Annotation of Genes and Transposable Elements in Plant Genomes. http://dawgpaws.sourceforge.net/
GNU General Public License, Version 3
http://www.gnu.org/licenses/gpl.html
THIS SOFTWARE COMES AS IS, WITHOUT ANY EXPRESS OR IMPLIED WARRANTY. USE AT YOUR OWN RISK.
James C. Estill <JamesEstill at gmail.com>
STARTED: 11/25/2008
UPDATED: 03/30/2009
VERSION: $Rev: 597 $
| cnv_repseek2gff.pl |