/ 
Bio-ToolBox-1.22
River stage zero No dependents
/ change_cluster_order.pl

NAME

change_cluster_order.pl

A script to change the order of gene cluster groups in a file.

SYNOPSIS

change_cluster_order.pl [--options...] <filename>

Options:
--in <filename>
--out <basename>
--order <numbers,range>
--keep
--version
--help

OPTIONS

The command line flags and descriptions:

--in <filename>

Specify either the input CDT or KGG file. The program assumes both files exist with the same basename and either a .kgg or .cdt file extension.

--out <basename>

Specify the output filename. By default it uses the base name of the input file. An appropriate .kgg and .cdt extension will be added.

---order <numbers,range>

Optionally provide the new order of gene cluster groups. A comma delimited list and/or range may be provided, without spaces. For example, 1-3,0,4,5.

--keep

Optionally keep the same cluster group numbers in the KGG file as the original, just in the new order. The default is to renumber the group numbers.

--version

Print the version number.

--help

Display this POD documentation.

DESCRIPTION

This program will change the order of gene cluster groups in KGG and CDT files. These files are generated by the Cluster algorithm and represent k-means clusters of genes based on collected experimental data. The cluster groups are defined in the KGG file, which is a simple text format with two columns, the gene ID and the GROUP number. Sometimes, when comparing data between two or more separate cluster analyses, it is useful to re-order the clusters such that similar clusters are ranked in a similar order. This script will accomplish that goal.

A KGG or CDT file is provided (both are required, but only one needs to be provided as a command line argument). The current order of the clusters is presented, and a new order is then requested. The new groups are re-labeled with new identifiers, or the old group numbers may be retained if requested.

CDT files may be visualized using the Java Treeview program, found at http://jtreeview.sourceforge.net.

AUTHOR

Timothy J. Parnell, PhD
Dept of Oncological Sciences
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT, 84112

This package is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0.