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draw_chromosome_gc.pl

Program for drawing gc profiles of long DNA contigs, e.g. whole chromosomes.
Just untar everything in your working directory and use.

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Usage:

draw_chromosome_gc.pl [parameters] seq png

Parameters:

-scale=#  : pixels / 1MB
-window=# : size of the sliding window
-gap=#    : minimum size of the gap to be drawn as grey box
            [number of Ns in row]
-ch=#     : name of the chromosome for the picture designation
-silent   : be really quiet
seq       : sequence (in fasta format)
png       : output name of png picture

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For running this program, you have to install perl (>5.0) and module GD.pm. 
Most Linux distributions (RedHat, Mandrake ..) have these in default 
instalation. If not, check http://cpan.perl.org.

Set up environment variable VERBOSE or DEBUG to 1 for verbal output
In bash you can use this command:
[hpaces@genomat]$ export VERBOSE=1

If you drop me an email with suggestions what else is needed I shall do
my best to improve the program

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Copying:

Recent version of this program can be found at http://genomat.img.cas.cz
Copyright (C) 2002 Jan Paces <hpaces@img.cas.cz>

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

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--> $Id: draw_chromosome_gc.txt,v 1.2 2002/01/08 08:28:00 hpaces Exp $ <--