MDscan.py -- Interface / Wrapper for MDscan program.
 
Download MDscan separately from author's website (see TAMO/paths.py for instructions)
At this time, we believe that MDscan is only available on the linux platform
 
This program is executable from the command line, and it runs the MDscan several times
with different motif widths.  Type "$TAMO/MD/MDscan.py" for options.
 
Copyright (2005) Whitehead Institute for Biomedical Research (except as noted below)
All Rights Reserved
 
Author: David Benjamin Gordon

Modules
		TAMO.seq.Fasta TAMO.MotifMetrics TAMO getopt math os re sys tempfile

Classes
		MDscan metaMDscan   class MDscan     Class for encapsulating (and processing) MDscan and its output     Methods defined here: __init__(self, file='', width=10, extra_args='', bgfile='')   class metaMDscan       Methods defined here: __init__(self, file='', width_start=6, width_stop=15, top_count=10, extra_args='', bgfile='')

Functions
		genomebg(infile, outfile) main() usage(txt='')

Data
		MDSCAN_DIR = '/etc/TAMOdata/MDprogs/MDscan/' MDSCAN_EXE = '/etc/TAMOdata/MDprogs/MDscan//MDscan.linux'