| batch_trf.pl |
batch_trf.pl - Run Tandem Repeat Finder in batch mode
This documentation refers to program version $Rev: 560 $
batch_trf.pl -i InDir -o OutDir
--indir # Path to the input directory
--outdir # Path to the output directory
This program runs the Tandem Repeat Finder program (TRF) in batch mode. Given a directory of fasta files, this will run the TRF program for all files in the directory.
Path of the directory containing the sequences to process.
Path of the directory to place the program output.
Path to a config file. This is a tab delimited text file indicating the required information for each of the databases to blast against. Lines beginning with # are ignored.
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 does not make use of a configuration file.
This program does not make use of variables in the user environment.
The batch_trf.pl program requires the Tandem Repeats Finder program. This program is available from: http://tandem.bu.edu/trf/trf.download.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 has been tested and is known to work with trf400.linux.exe
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: 11/10/2008
UPDATED: 03/24/2009
VERSION: $Rev: 560 $
| batch_trf.pl |