| batch_genscan.pl |
batch_genscan.pl - Run genscan and parse results to a gff format file.
This documentation refers to batch_genscan.pl version $Rev: 556 $
batch_genscan.pl -i DirToProcess -o OutDir
-i, --indir # Directory of fasta files to process
-o, --outdir # Path to the base output directory
Run the GENSCAN gene prediction program in batch mode. This will run genscan as well as convert the output to gff format.
Path of the directory containing the sequences to process.
Path of the directory to place the program output.
The full path to the genscan binary.
The full path to the library file.
Path to a file that will be used to log program status. If the file already exists, additional information will be concatenated to the existing file.
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 without doing the system commands.
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.
The batch_genscan.pl program currently does not make use of any external configuration files.
The following environment variables may be used to designate the full path to the GENSCAN binary and the default library path to use.
The path to the genscan binary file.
The path to the default library to use for gene predictions using genscan.
The following example shows the lines that would need to be added to your .bashrc file in the bash shell to specify the location of the genscan binary and the Maize library file in your home directory.
export DP_GENSCAN_BIN='/home/yourname/apps/genscan/genscan'
export DP_GENSCAN_LIB='/home/yourname/apps/genscan/Maize.smat'
This program obviously requires the GENSCAN gene model prediction program. Information for downloading the GENSCAN program is available from: http://genes.mit.edu/GENSCANinfo.html
This module is required to copy the results.
This module is required to accept options at the command line.
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
The config file must have UNIX formatted line endings. Because of this any config files that have been edited in programs such as MS Word must be converted to a UNIX compatible text format before being used with batch_blast.
The batch_genscan.pl 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: 07/31/2007
UPDATED: 03/24/2009
VERSION: $Rev: 556 $
| batch_genscan.pl |