COMMAND-LINE USAGE
* Bipartite structured motif discovery tool: BiPad version 1.10 
* (C) 2003-2009 Children's Mercy Hospitals, All Rights Reserved
*
* Author: Dr. Chengpeng Bi
* Algorithm implemented: GNU C/C++ compiler in Linux, Unix or MacOS
*
* USAGE: bipad [options] dnaseqs.txt [options] [> output filename]
* OPTIONS:
*
*  Toggles (no values associated) 
*       -h  help: print this text
*       -1  ("one") just examine forward strand (default: both strands)
*       -2  ("two") build two-block (i.e. bipartite) model (default: one-block)
*       -d  switch on printing the gap distance distribution
*       -D  turn off calculating penalty 
*       -f  switch on printing full alignments
*       -i  switch on printing information weigth matrix (i.e. PWM)
*       -M  turn on mute (disable all printing)
*       -P  turn on printing search progress
*       -q  switch off uniform pseudocounts (default: uniform distribution)
*       -u  switch off uniform background (disabled)
*       -z  turn on ZOOPS (default: OOPS)
*
*  Set values
*       -T  [project title] (default: TFBS)
*       -a  [minimum gap size] (default: 0 bp)
*	-A  position assignment file
*       -b  [maximum gap size] (default: 6 bp)
*       -B  [maximum printing gap] (default: 20 bp)
*       -j  [flanking bases] for right motif (default: 0)
*       -k  [flanking bases] for left  motif (default: 0)
*       -l  [width] for left motif (default: 6 bp)
*       -m  [width] for right motif (deafult: 6 bp)
*       -n  [width] for one-block motif (default: 6 bp)
*       -p  [total pseudocounts] (deafult: 1.5)
*       -y  [number of iterations] (default: 10)
*
* EXAMPLE:
* bash-2.05$ bipad -2D -l8 -m8 -dis -a3 -b9 -y500 -T'CRP sites' crp.txt