1 Author: Martin Asser Hansen - Copyright (C) - All rights reserved
3 Contact: mail@maasha.dk
7 License: GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)
9 Description: Generate a plot of PhastCons profiles based on chromosome coordinates in stream.
11 Usage: ... | plot_phastcons_profiles [options]
13 Options: [-x | --no_stream] - Do not emit records.
14 Options: [-o <file> | --data_out=<file>] - Write result to file.
15 Options: [-g <genome> | --genome=<genome>] - Genome from which to obtain PhastCons info.
16 Options: [-m | --mean] - Calculate a mean profile.
17 Options: [-M | --median] - Calculate a median profile.
18 Options: [-f <int> | --flank=<int>] - Include flanking PhastCons scores.
19 Options: [-t <string> | --terminal=<string> - Terminal for output: dumb|post|svg - Default=dumb
20 Options: [-d <string> | --direction=<string> - Direction of matches to plot: both|forward|reverse - Default=both
21 Options: [-T <string> | --title=<string>] - Set plot title.
22 Options: [-X <string> | --xlabel=<string>] - Set x-axis label.
23 Options: [-Y <string> | --ylabel=<string>] - Set y-axis label.
24 Options: [-I <file> | --stream_in=<file>] - Read input from stream file - Default=STDIN
25 Options: [-O <file> | --stream_out=<file>] - Write output to stream file - Default=STDOUT
27 Examples: ... | plot_phastcons_profiles -x -g dm3 -f 50 - Create plot of all profiles including 50 flanking scores.
28 Examples: ... | plot_phastcons_profiles -x -g dm3 -f 50 -m - Create a mean plot of all profiles including 50 flanking scores.