Author:         Martin Asser Hansen - Copyright (C) - All rights reserved

Contact:        mail@maasha.dk

Date:           January 2008

License:        GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)

Description:    Generate a plot of PhastCons profiles based on chromosome coordinates in stream.

Usage:          ... | plot_phastcons_profiles [options]

Options:  [-x          | --no_stream]          -  Do not emit records.
Options:  [-o <file>   | --data_out=<file>]    -  Write result to file.
Options:  [-g <genome> | --genome=<genome>]    -  Genome from which to obtain PhastCons info.
Options:  [-m          | --mean]               -  Calculate a mean profile.
Options:  [-M          | --median]             -  Calculate a median profile.
Options:  [-f <int>    | --flank=<int>]        -  Include flanking PhastCons scores.
Options:  [-t <string> | --terminal=<string>   -  Terminal for output: dumb|post|svg                  -  Default=dumb
Options:  [-d <string> | --direction=<string>  -  Direction of matches to plot: both|forward|reverse  -  Default=both
Options:  [-T <string> | --title=<string>]     -  Set plot title.
Options:  [-X <string> | --xlabel=<string>]    -  Set x-axis label.
Options:  [-Y <string> | --ylabel=<string>]    -  Set y-axis label.
Options:  [-I <file>   | --stream_in=<file>]   -  Read input from stream file  -  Default=STDIN
Options:  [-O <file>   | --stream_out=<file>]  -  Write output to stream file  -  Default=STDOUT

Examples:  ... | plot_phastcons_profiles -x -g dm3 -f 50    -  Create plot of all profiles including 50 flanking scores.
Examples:  ... | plot_phastcons_profiles -x -g dm3 -f 50 -m -  Create a mean plot of all profiles including 50 flanking scores.