vennseq.pl


NAME

vennseq.pl - Venn diagram overlap of sequence features


SYNOPSIS

Usage

    vennseq.pl -i InputFastaFile.fasta -o OutputFile -d FeatureFileDir
               -f tab

Required Options

    -i       # Fasta file being annotated
    -o       # Output file
    -d       # Feature file directory
    -f       # Format of the annotation data [gff]
           
=head1 DESCRIPTION

Creates a Venn Diagram comparing the overlap of sequence features along a query sequence. The purpose is to allow me to visualize the overlap of Repeat Databases or gene models along a BAC.


REQUIRED ARGUMENTS

-i

Path to the sequence file in fasta format.

-o

Path to the output file in the Venn text file.

-d

Directory containing sequence features.


OPTIONS

-f,--format

The feature file format. This must be one of ( tab | blast | gff ). Currently only tab delim blast hits are supported. This is set to gff default.

-s,--svg-out

Path to a svg format vector file of the Venn diagram. This will produce a svg file at this path, otherwise to svg file is created.

--venn-master

The directory containing the VennMaster program.

--no-vm

This will do the anlysis of the suquence features, and write the analysis to STDOUT without using VennMaster to visualize the results.

--java-path

The path to the java binary. By default, this program will use 'java' and assume that the java path you want to use is defined in your PATH.

--seq-id

The identifier to use for the sequence id

--seq-len

This is an alternative to providing a sequence file to determine the sequence length from. This allows you to define the lenght of the sequence that the features are being mapped onto.

--debug

Run the program in debug mode.

--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.

--verbose

Run the program with maximum output.


DIAGNOSTICS

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


CONFIGURATION AND ENVIRONMENT

Configuration File

This program does not require a configuration file and does not

Environment Variables

The following variables may be dfined in the user environment.


DEPENDENCIES

Required Software

Required Perl Modules

This program does not require Perl modules beyond those modules included in a normal installation of Perl.


BUGS AND LIMITATIONS

Bugs

Limitations


SEE ALSO

The vennseq.pl program is part of the DAWGPAWS package of genome annotation programs. See the DAWGPAWS 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

THIS SOFTWARE COMES AS IS, WITHOUT ANY EXPRESS OR IMPLIED WARRANTY. USE AT YOUR OWN RISK.


AUTHOR

James C. Estill <JamesEstill at gmail.com>


HISTORY

Started: 03/06/2007

Updated: 04/06/2009

Version: $Rev: 609 $

 vennseq.pl