fasta_merge.pl


NAME

fasta_merge.pl - Merge all fasta files in a directory


VERSION

This documentation refers to program version $Rev: 613 $


SYNOPSIS

Usage

   fasta_merge.pl -i in_dir/ -o out_file.fasta

Required Arguments

    -i,--indir    # Path to the directory containing the fasta files
    -o,--outfile  # Path to the fasta format outfile
                  # Writes output to standard output otherwise


DESCRIPTION

Given a directory, merge all of the fasta files in the directory into a single fasta file.


ARGUMENTS

-i,--indir

Path to the input directory containing the fasta files.

-o,--outfile

Path to the fasta file that will be produced. If an output file is not specified at the command line, the output will be writtent to STDOUT.


OPTIONS

--verbose

Run the program in verbose mode, this will write the maximum amount of output to STDERR.

--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

The error message that can be generated will be listed here.


DEPENDENCIES

This program does not depend on external software or perl modules outside of those included in a typcial installation of perl.


BUGS AND LIMITATIONS

Bugs

Limitations


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 LESSER GENERAL PUBLIC LICENSE

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.


AUTHOR

James C. Estill<lt>JamesEstill at gmail.com>


HISTORY

STARTED: 08/20/2006

UPDATED: 04/06/2009

VERSION: $Rev: 613 $

 fasta_merge.pl