batch_tenest.pl


NAME

batch_tenest.pl - Run TENest in batch mode


VERSION

This documentation refers to program version $Rev: 564 $


SYNOPSIS

Usage

    batch_tenest.pl -i indir -o outdir

Required Arguments

    -i,--indir         # Dir containing fasta files to process 
    -o,--outdir        # Dir to place the output in


DESCRIPTION

Runs the program TE Nest in batch mode. This will run TE Nest for all fasta files located in the input directory.


REQUIRED ARGUMENTS

-i,--indir

Path to the directory containing the input files to annotate with TEnest. These files must be in the fasta format.

-o,--outdir

Path to the base output directory to place the batch_tenest.pl output.


OPTIONS

--org

The organism database to use. The default organism database is maize.

--blast-dir

The directory for wu blast. If this directory is not specified at the command line, batch_tenest.pl will assume that this is at /usr/local/genome/wu_blast/

--tenest-dir

The directory that the TE Nest program is located in. If this directory is not specified, batch_tenet.pl will assume that the TE Nest program is locate in your home directory at $HOME/apps/te_nest/

--usage

Short overview of how to use program from command line.

--help

Show program usage with summary of options.

--version

Show program version.

--man

Show the full program manual. This uses the perldoc command to print the POD documentation for the program.

-q,--quiet

Run the program with minimal output.


DIAGNOSTICS

TENest.pl does not exist at: /some/directory/

The TENest.pl program does not exist at the directory you specified or in the directory that the program assumes it to be in. The best way to make sure this works is to specify a directory using the --tenest-dir option.

Can't open directory: /your/input/directory/

The input directory that you specified by the -i file has either been typed in incorrectly, the path you entered does not exist, or you do not have read access to that directory.

ERROR: No fasta files were found in the input directory

Currently this program assumes that all fasta files end with the fasta or fa extension. It is possible that you have fasta files in the input directory, but they do not have the *.fasta or *.fa file names.


CONFIGURATION AND ENVIRONMENT

This program does not make use of configuration files or variables set in the user environment.


DEPENDENCIES

Required Software

TE Nest

This program requires the installation of TE Nest. This program is available from: http://www.public.iastate.edu/~imagefpc/Subpages/te_nest.html

Required Databases

This program requires an organism database is the TE Nest format. This databases are downloadable from: http://www.public.iastate.edu/~imagefpc/Subpages/te_nest.html


BUGS AND LIMITATIONS

Bugs

Limiations


SEE ALSO

This 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.


REFERENCE

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/


LICENSE

GNU General Public License, Version 3

http://www.gnu.org/licenses/gpl.html


AUTHOR

James C. Estill <JamesEstill at gmail.com>


HISTORY

STARTED: 09/29/2008

UPDATED: 03/24/2009

VERSION: $Rev: 564 $

 batch_tenest.pl