| batch_hardmask.pl |
batch_hardmask.pl - Hardmask a directory of softmasked fasta files.
This documentation refers to batch_hardmask version $Rev: 603 $
batch_hardmask.pl -i DirToProcess -o OutDir
-i, --indir # Directory of fasta files to process
-o, --outdir # Path to the base output directory
Given a directory of FASTA formatted sequence files that have been softmasked, this will replace lowercase masked characters (a,g,c,t) with a masked character. You can choose from a limited set of characters to mask with (x,X,n,N).
Path of the directory containing the sequences to process.
Path of the directory to place the program output.
Single letter to mask with. Valid options are: [ N | n | X | x ]
The new outfile extension to use. Default value is .hard.fasta
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.
This program does not currently depend on any external configuration files or and variables set in the user environment.
The batch_hardmask.pl program is not dependent on any external software.
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
Input files will only be recognized as fasta files if they have the *.fa or *.fasta extension.
The batch_hardmask.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: 07/19/2007
UPDATED: 03/24/2009
VERSION: $Rev: 603 $
| batch_hardmask.pl |