Usage: XClust.py parameter_filename input_filename output_filename

Wrapper for XClust algorithm

Note: The class labels will have the extension you specify on the command line and the two xclust intermediate files if saved will have a .cdt and .gtr extension.

Depends on the following environment variables: XCLUST_COMMAND (e.g., /proj/cluster_gazing2/bin/xclust)

Brief Algorithm Description:

See: Eisen et. al. 1998, PNAS 95 (25) for a description of xclust we have implemented various methods to construct a partioning based of the phylogenetic tree output from xclust

Required Parameters: (note: the list enclosed in the brakets are possible values each one of parameters can take )

transform_method = [log, none] distance_metric = [correlation,correlation_centered, euclidean] cluster_on = [columns, rows]

rows : cluster Genes columns: cluster conditions

agglomerate_method = [none, size, clusterNumber]

none - do not agglomerate, just generate the normal xclust output files

size - perform a size threshold agglomeration. Starting at the root recurse through the tree attempting to agglomerate at each node stopping only when the number of genes in the agglomerated sub-tree is less then the parameter "size_threshold"

clusterNumber - return as close to K clusters as possible using the "size" agglomeration method to partition the tree

Optional / Dependent Parameters:

size_threshold = <x> (required if agglomerate_method = size)

where x is an interger and 0 < x <= # Of Data Vectors see above for a complete description.

k = <x> (required if agglomerate_method = "clusterNumber" where x is the number of clusters you'd like

save_intermediate_files = [yes, 'no'] (required if agglomerate_method doesn't equal "none")

if you choose yes, the original xclust files (both the cdt and gtr) will be saved. Otherwise they will be deleted.

use_intermediate_files = [yes, 'no'] if yes, will load an existing GTR/CTD file instead of building the tree again. Will detemine the intermediate filenames either from the input file (if run from the shell wrapper) or the save_intermediate_files_base and results_dir optional parameters

save_intermediate_files_base = filename The base filename for intermidate file (ie, no GTR or CTD file)

results_dir Location of results.