| cnv_game2gff3.pl |
cnv_game2gff3.pl - Convert game.xml to gff3 format
This documentation refers to program version $Rev: 610 $
cnv_game2gff3.pl -i infile.xml -o outfile.gff
--infile # Path to the input file or direcotry
--outfie # Path to the output file
This program can covert game.xml files to the gff3 format. This script is essentially a wrapper around the Apollo genome annotation editor program, so Apollo is require for this script to work. It can convert a single file at a time, or all game.xml files in a directory.
Path of the input file or directory. If the input path is a file, the single file will be converted to the gff3 with a file name specified by the --outfile option. If an entire directory of files is being specified by the -i option, all of the files ending in xml will be be converted to gff format. The gff file will be generated in the input directory, and the files will have the existing name with gff appended.
Path of the output file. If the input path is a directory, then this argument is not needed.
Path to the apollo binary. By default, the program assumes that the directory containing the apollo program is included in your PATH. If this is not the case, you will need to specify the location of the apollo program using the -ap-bin variable.
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 in verbose mode.
To convert a single game.xml file to gff3 format, you would use the following command:
cnv_game2gff3.pl -i HEX001.game.xml -o HEX001.gff
This will result in a single file name HEX001.gff in the path specified by the -o argument.
To convert an entire directory of game.xml files to the gff3 format, simply specify the directory containing the game.xml files with the -i argument:
cnv_game2gff3.pl -i annotation_dir/
This will find all files with names ending in xml, and will convert those files to the gff3 format. The .gff extension will be added on to the existing file name. For example, the following list shows the name of game files and the name of the gff files that would be created:
Game File GFF File Created
HEX001.game.xml HEX001.game.xml.gff
HEX002.game.xml HEX001.game.xml.gff
HEX003.game.xml HEX003.game.xml.gff
The gff files will be created in the same directory as the game.xml files. The original files will not be overwritten in this process.
The following information includes error message you may encounter when using this program, and information on possible solutions to these errors.
This program that the files you want to convert will be named with the xml extension, and that all files that end with xml are game.xml files. If you have files in this directory that you need to convert, they must all end with xml.
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 uses the Apollo program to convert from game.xml to gff3 format. The Apollo program can be obtained at: http://apollo.berkeleybop.org/current/index.html
This program does not make use of Perl modules beyond the standard modules included in basic installations of Perl.
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 is completely dependent on a local installation of the Apollo program since it depends on Apollo to do the conversion.
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: 02/17/2009
UPDATED: 03/24/2009
VERSION: $Rev: 610 $
| cnv_game2gff3.pl |