1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283
|
#!/usr/bin/env perl
=pod
=head1 NAME
____ _
/ ___(_)_ __ ___ ___ ___
| | | | '__/ __/ _ \/ __|
| |___| | | | (_| (_) \__ \
\____|_|_| \___\___/|___/
round is good
circos - generate publication-quality, circularly-composited plots
of data and annotations layered on chromosome ideograms
=head1 SYNOPSIS
circos -conf circos.conf [-silent] [-debug] [-help] [-man]
=head1 DESCRIPTION
This is a command line interface to Circos. Most settings are meant to be passed using a configuration file.
All command line options listed below can be defined in the configuration file. Defining them on the command line is useful when using a configuration template for many images.
=head1 OPTIONS
=head2 Configuration
=over
=item -configfile FILE
Name of configuration file. This is required.
=back
=head2 Ideograms
=over
=item -chromosomes STRING
=item -chromosomes_order STRING
=item -chromosomes_scale STRING
=item -chromosomes_radius STRING
Defines list, order, scale and radius of ideograms.
=back
=head2 Output Format
=over
=item -png
=item -24bit
=item -svg
Toggles output of PNG and SVG files.
When using transparency, make sure that PNG output is 24-bit.
=back
=head2 Output Paths
=over
=item -outputdir DIR
=item -outputfile FILE
Change the output directory and filename.
=back
=head2 Input Format
=over
=item -file_delim DELIMITER
Specify the file delimiter for all input data files. By default this
is a space. Use a tab if you want to have multi-word records in the
data files (e.g. multi word labels).
=back
=head2 Custom Fields
=over
=item -usertext1 STRING
=item -usertext2 STRING
=item -usertext3 STRING
=item -usertext4 STRING
Custom fields that can be used to change any string in the
configuration file. The fields are referenced in the configuration
file using C<__$CONF{usertext1}__>, etc. This is useful if you are
creating multiple versions of an image with different settings.
For example, in the configuration file you can have
<link segdup>
radius = __$CONF{usertext1}__r
and then call Circos
bin/circos ... -usertext1 0.9
bin/circos ... -usertext1 0.5
=back
=head2 Ticks
=over
=item -show_ticks, -noshow_ticks
=item -show_tick_labels, -noshow_tick_labels
Toggle display of ticks and tick labels.
=back
=head2 Image Maps
=over
=item -image_map_use
=item -image_map_name MAPNAME
=item -image_map_file FILE
=item -image_map_missing_parameter { exit | removeparam | removeurl }
Controls image map settings. See
http://mkweb.bcgsc.ca/circos/tutorials/lessons/image_maps
=back
=head2 Debugging
=over
=item -silent
Generate no reporting.
=item -version
Print the version.
=item -debug
Turn on debugging output.
=back
=cut
use strict;
use warnings;
use FindBin;
use Getopt::Long;
use Pod::Usage;
use lib "$FindBin::RealBin";
use lib "$FindBin::RealBin/../lib";
use lib "$FindBin::RealBin/lib";
use Circos;
use Circos::Debug;
my %OPT;
GetOptions(\%OPT,
'imagemap',
'chromosomes=s',
'chromosomes_display_default!',
'chromosomes_order=s',
'chromosomes_scale=s',
'chromosomes_radius=s',
'show_ticks!',
'show_tick_labels!',
'outputdir=s',
'outputfile=s',
'usertext1=s',
'usertext2=s',
'usertext3=s',
'usertext4=s',
'tagname',
'png!',
'svg!',
'file_delim=s',
'background=s',
'image_map_name=s',
'image_map_file=s',
'image_map_use',
'image_map_missing_parameter',
'color_cache_rebuild',
'color_cache_static',
'configfile=s',
'cdump:s',
'cdebug',
'randomcolor:s',
'help',
'man',
'silent',
'paranoid!',
'warnings!',
'fakeerror=s',
'debug+',
'debug_group=s',
'version',
);
pod2usage() if $OPT{'help'};
pod2usage(-verbose=>2) if $OPT{'man'};
$OPT{debug_group} .= "conf" if $OPT{cdebug};
Circos->run(%OPT);
# -------------------------------------------------------------------
=pod
=head1 AUTHOR
Martin Krzywinski E<lt>martink@bcgsc.caE<gt> L<http://mkweb.bcgsc.ca>
=head1 RESOURCES
L<http://mkweb.bcgsc.ca/circos>
=head1 CITING
If you are using Circos in a publication, please cite as
Krzywinski, M., J. Schein, I. Birol, J. Connors, R. Gascoyne,
D. Horsman, S. Jones, and M. Marra. 2009. Circos: an Information
Aesthetic for Comparative Genomics. Genome Res 19:1639-1645.
=head1 CONTRIBUTORS
Ken Youens-Clark E<lt>kyclark@gmail.comE<gt>
=head1 SEE ALSO
Hive plots L<http://www.hiveplot.com>
=head1 COPYRIGHT & LICENSE
Copyright 2004-2012 Martin Krzywinski, all rights reserved.
This file is part of the Genome Sciences Centre Perl code base.
This script 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 script 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 script; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
=cut
|