| batch_repmask.pl |
batch_repmask.pl - Run RepeatMasker and parse results to a GFF format file.
This documentation refers to program version $Rev: 599 $
batch_repmask.pl -i DirToProcess -o OutDir -c ConfigFile
-i, --indir # Directory of fasta files to process
-o, --outdir # Path to the base output directory
-c, --config # Path to the config file
Runs the RepeatMasker program for a set of input FASTA files against a set of repeat library files & then converts the repeat masker *.out file into the GFF format and then to the game XML format for visualization by the Apollo genome anotation program.
Path of the directory containing the sequences to process.
Path of the directory to place the program output.
Configuration file that lists the database names and paths of the fasta files to use as masking databases.
The number of processors to use for RepeatMasker. Default is one.
The repeatmasker engine to use: [crossmatch|wublast|decypher]. The default is to use the crossmatch engine.
Use the apollo program to convert the file from gff to game xml. The default is not to use apollo.
The full path to the RepeatMasker binary.
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.
Run the program with minimal output.
Run the program without doing the system commands.
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.
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 major configuration file for this program is the list of datbases indicated by the -c flag.
This file is a tab delimited text file. Lines beginning with # are ignored.
EXAMPLE
#------------------------------------------------------------- # DBNAME DB_PATH #------------------------------------------------------------- TREP_9 /db/repeats/Trep9.nr.fasta TIGR_Trit /db/repeats/TIGR_Triticum_GSS_Repeats.v2.fasta TREP_9_Clip /db/repeats/Trep9.nr.fasta -is_clip # END
The columns above represent the following
The name of the repeat library This will be used to name the output files from the analysis and to name the data tracks that will be used by Apollo.
The path to the fasta format file containing the repeats.
An optional third col may also be included. This can include addiontal options to include in the RepeatMasker run. This should include valid RepeatMasker options separated by spaces. You can type RepeatMasker --help for the full list of options accepted by your version of RepeatMasker. In the example above, the -is_clip option will clip any E. coli insertion elements that are contained in the contigs.
The RepeatMasker program can be download at: (http://www.repeatmasker.org/)
The Apollo Genome Annotation Curation tool can be downloaded at http://www.fruitfly.org/annot/apollo/ .
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
This program has been tested with RepeatMasker v 3.1.6
Currently this program does not make use of variables in the user environment. However, it would be useful to define program paths and some common options in the environment.
The batch_repmask.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
THIS SOFTWARE COMES AS IS, WITHOUT ANY EXPRESS OR IMPLIED WARRANTY. USE AT YOUR OWN RISK.
James C. Estill <JamesEstill at gmail.com>
STARTED: 04/10/2006
UPDATED: 03/24/2009
VERSION: $Rev: 599 $
| batch_repmask.pl |