File: circos

package info (click to toggle)
circos 0.61-3
  • links: PTS, VCS
  • area: main
  • in suites: wheezy
  • size: 28,368 kB
  • sloc: perl: 13,724; sh: 28; makefile: 13
file content (283 lines) | stat: -rwxr-xr-x 5,532 bytes parent folder | download
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