| vennseq.pl |
vennseq.pl - Venn diagram overlap of sequence features
vennseq.pl -i InputFastaFile.fasta -o OutputFile -d FeatureFileDir
-f tab
-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.
Path to the sequence file in fasta format.
Path to the output file in the Venn text file.
Directory containing sequence features.
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.
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.
The directory containing the VennMaster program.
This will do the anlysis of the suquence features, and write the analysis to STDOUT without using VennMaster to visualize the results.
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.
The identifier to use for the sequence id
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.
Run the program in debug mode.
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.
Run the program with maximum output.
Error messages generated by this program and possible solutions are listed below.
This program does not require a configuration file and does not
The following variables may be dfined in the user environment.
This is the directory where the VennMaster program is located This option can also be defined wit the --venn-master option at the command line.
This is the path of the java binary that you want to use to run the VennMaster program. If this is not specified in the user environment, this will use 'java' as defined in the PATH variable. This option can also be defined with the --java-path option at the command line.
This is the amount of memory to allot to the VennMaster program If this is not specified, the program will use 512 GB memory. This option can also be defined with the --java-mem option at the command line.
This progra requires the VennMaster program http://www.informatik.uni-ulm.de/ni/staff/HKestler/vennm/doc.html.
This program does not require Perl modules beyond those modules included in a normal installation of Perl.
If you find a bug with this software, file a bug report on the DAWGPAWS Sourceforge website: http://sourceforge.net/tracker/?group_id=204962
I have only tested this will VennMaster on the Mac OS 10.5.
For gff files, the separate sources must be in separate gff files. Currently sources defined in the second colum will be regarded as the same source if they are in the same gff file.
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.
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
THIS SOFTWARE COMES AS IS, WITHOUT ANY EXPRESS OR IMPLIED WARRANTY. USE AT YOUR OWN RISK.
James C. Estill <JamesEstill at gmail.com>
Started: 03/06/2007
Updated: 04/06/2009
Version: $Rev: 609 $
| vennseq.pl |