batch_hardmask.pl


NAME

batch_hardmask.pl - Hardmask a directory of softmasked fasta files.


VERSION

This documentation refers to batch_hardmask version $Rev: 603 $


SYNOPSIS

Usage

    batch_hardmask.pl -i DirToProcess -o OutDir

Required Arguments

    -i, --indir    # Directory of fasta files to process
    -o, --outdir   # Path to the base output directory


DESCRIPTION

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).


REQUIRED ARGUMENTS

-i,--indir

Path of the directory containing the sequences to process.

-o,--outdir

Path of the directory to place the program output.


OPTIONS

--m,mask

Single letter to mask with. Valid options are: [ N | n | X | x ]

--ext

The new outfile extension to use. Default value is .hard.fasta

--logfile

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.

--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.

--test

Run the program without doing the system commands.


DIAGNOSTICS

Error messages generated by this program and possible solutions are listed below.

ERROR: No fasta files were found in the input directory

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.

ERROR: Could not create the output directory

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.


CONFIGURATION AND ENVIRONMENT

This program does not currently depend on any external configuration files or and variables set in the user environment.


DEPENDENCIES

Required Software

Required Perl Modules


BUGS AND LIMITATIONS

Bugs

Limitations


SEE ALSO

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.


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: 07/19/2007

UPDATED: 03/24/2009

VERSION: $Rev: 603 $

 batch_hardmask.pl