| cnv_gff2game.pl |
cnv_gff2game.pl - Convert a gff file to game xml
This documentation refers to program version $Rev: 611 $
cnv_gff2game.pl -i InFile.fasta -g GffFile.gff -o OutFile.game.xml
-i # Path to the fasta file the gff refers to
-g # Path to the gff file to convert
-o # Path to the output game.xml file
Converts gff foramt files to the game.xml format. This program uses the Apollo genome annotation program to do this conversion, so you must have Apollo installed for this script to work
Path of the input fasta filefile.
Path of the input gff file
Path of the output game xml file.
=back
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.
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.
This program does not make use a configuration file.
The following variables can be defined in the user environment:
The location of the apollo binary file. This is the path used to lauch the Apollo genome annotation program. If not specified in the user environment, this will attempt to call 'apollo'. The path may also be specified using the --ap-path option at the command line.
This program requires that apollo be installed on the local machine since apollo is being used as the engine to do the conversion between formats. Apollo is available from: http://apollo.berkeleybop.org/current/index.html
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
New versions of Apollo come out on a regular basis, and older versions of Apollo are not arcived. I am therefore limited to testing this program to versions of Apollo that are extant at the time this script was written. This is known to work on Apollo version 1.6.5.
The command line interface from Apollo does not appear to work on text only terminals.
In general the cnv scripts are designed to support input from STDIN and output from STDOUT. The gff to game converter relies on Apollo, and currently does not support the STDIN and STOUT. :(
This program is part of the DAWG-PAWS package of genome annotation programs. See the DAWG-PAWS web page ( http://dawgpaws.sourceforge.net/ ) or the Sourceforge project page ( http://sourceforge.net/projects/dawgpaws ) for additional information about this package.
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
James C. Estill <JamesEstill at gmail.com>
STARTED: 02/09/2007
UPDATED: 03/24/2009
VERSION: $Rev: 611 $
| cnv_gff2game.pl |