| batch_geneid.pl |
batch_geneid.pl - Run the genid program in batch mode.
This documentation refers to program version $Rev: 554 $
batch_geneid.pl -i InDir -o OutDir
--infile # Path to the input directory
--outfie # Path to the output directory
--param # Path to the GeneID parameter file
This program will run the geneid gene annotation program on a directory of fasta files.
Path of the directory containing the sequences to process.
Path of the directory to place the program output.
Path to the GeneID Parameter file.
The path to the geneid program. If a path is not supplied at the command line the program will assume that the directory containing the geneid program is included in the user PATH parameter.
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 maximum output.
Run the program with minimal output.
Run the program without doing the system commands. This will test for the existence of input files.
Error messages generated by this program and possible solutions are listed below.
The input directory does not contain fasta files in the expected format. This could happen because you gave an incorrect path or because your sequence files do not have the expected *.fasta extension in the file name.
The output directory could not be created at the path you specified. This could be do to the fact that the directory that you are trying to place your base directory in does not exist, or because you do not have write permission to the directory you want to place your file in.
This program currently does not make use of a configuration file.
This program does not make use of variables in the user environment.
This program requies the geneid gene annotation program to work. This program is available from: http://genome.imim.es/software/geneid/index.html
This module is required to accept options at the command line.
Any known bugs and limitations will be listed here.
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 known to work on genid version March_1_2005. This program has not been tested with other versions of geneid.
The 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
THIS SOFTWARE COMES AS IS, WITHOUT ANY EXPRESS OR IMPLIED WARRANTY. USE AT YOUR OWN RISK.
James C. Estill <JamesEstill at gmail.com>
STARTED: 11/06/2008
UPDATED: 03/24/2009
VERSION: $Rev: 554 $
| batch_geneid.pl |