| ltrstruc_prep.pl |
ltrstruc_prep.pl - Prepare files needed to do a run in LTR_STRUC
This documentation refers to program version $Rev: 587 $
ltrstruc_prep.pl -i InDir -o OutDir
-i, --indir # Directory of fasta files to process
-o, --outdir # Path to the base output directory
Given a directory of fasta files with UNIX line endings ltrstruc_prep.pl will create DOS formated files with the txt extension. This will also create the flist.txt file.
Path of the input file.
Path of the output 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.
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 ltrstruc_prep.pl program currently does not require an external configuration file or make use of variables defined in the user's environment.
This program is designed to create files required for the LTR_Struc program. This program is available for download from: http://www.genetics.uga.edu/retrolab/data/LTR_Struc.html
This module is required to copy the BLAST 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
There are currently no known major limitations to using this program.
The ltrstruc_prep.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: 09/24/2007
UPDATED: 12/11/2007
VERSION: $Rev: 587 $
| ltrstruc_prep.pl |