change_cluster_order.pl
A script to change the order of gene cluster groups in a file.
change_cluster_order.pl [--options...] <filename>
Options: --in <filename> --out <basename> --order <numbers,range> --keep --version --help
The command line flags and descriptions:
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.
Specify the output filename. By default it uses the base name of the input file. An appropriate .kgg and .cdt extension will be added.
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.
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.
Print the version number.
Display this POD documentation.
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.
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 Artistic License 2.0.
To install Bio::ToolBox, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::ToolBox
CPAN shell
perl -MCPAN -e shell install Bio::ToolBox
For more information on module installation, please visit the detailed CPAN module installation guide.