| batch_findltr.pl |
batch_findltr.pl - Run the find_ltr.pl program in batch mode.
This documentation refers to program version $Rev: 557 $
batch_findltr.pl -i InDir -o OutDir -c Config.cfg [--gff]
--indir # Path to the input directory of fasta files
--outdir # Path to the base output directory
--config # Config file containg batch_findltr.pl paramaters
--gff # Produce GFF formatted output
Runs the program find_ltr.pl in batch mode. This makes use of a modified version of the find_ltr.pl program that takes changes to the LTR finding parameters at the command line.
Path of the input directory. This is the directory that contains all of the fasta files to anlayze. The fasta files should all end with the fasta extension to recognized.
Path of the output directory. This is the base directory that will hold all of the batch_findltr.pl output
Path of the config file that contains the model options for running find_ltr. This config file is a white space delimited text file that should be in the following format.
#---------------------------------------------------------------+ #1 2 3 4 5 6 7 8 9 10 | #---------------------------------------------------------------+ Def 40 1100 16000 40 100 1000 500 700 0.0000000001 Alt 40 1100 1800 40 100 1000 500 400 0.00001
More information about this file is available under configuration and environment heading below.
Location of the find_ltr.pl program. This option can also be set in the users envrionment. See Configuration and Environment below.
Run the program with minimal output.
Run the program in verbose mode.
Produce gff formatted output of the results.
Run the program in test mode. The find_ltr.pl program will not be run, but the location of source files, binaries, will be checked and the outupt directories will be created.
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 configuration file in batch_findltr.pl specifies the options for running the find_ltr.pl program. This is a white space delimited text file. All lines starting with the # symbol will be treated as comments. An example of a config file is below:
#---------------------------------------------------------------+ #1 2 3 4 5 6 7 8 9 10 | #---------------------------------------------------------------+ Def 40 1100 16000 40 100 1000 500 700 0.0000000001 Alt 40 1100 1800 40 100 1000 500 400 0.00001
These 10 columns represents the following information:
Base_name for the parameter set. This set name will be used to name the output file, and will be added to the output of the gff output file. DO NOT INCLUDE SPACES IN NAMES
Minimum Length MEM
Mimimum distance between MEMs
Maximum distance between MEMs
Maximu gap between MEMs
Minimum length of the LTR
Maximum length of the LTR
Range Bin
Minimum length of ORF
Mac E value of HMM Hit
As an alternative to specifying the full path of the find_ltr program with the --fl-path option, the path of the find_ltr program can be specified in the users environment. For example in bash shell, add the following line to your .bashrc
export FIND_LTR_PATH='/usr/local/genome/find_ltr.pl'
assuming that the find_ltr.pl program is in the /usr/local/genome/ directory.
A modified version of the find_ltr.pl program is required.
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
The batch_finltr.pl program requies a modified version of the batch_ltr.pl program that accepts parameters from the command line.
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_findltr.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: 09/13/2007
UPDATED: 03/24/2009
VERSION: $Rev: 557 $
| batch_findltr.pl |