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
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
|
cirdna
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Draw circular map of DNA constructs
Description
cirdna draws circular maps of DNA constructs. It uses graphical shapes
including ticks, ranges, and blocks to represent genetic markers (e.g,
genes and ESTs) and places them according to their position in a DNA
fragment. The markers can be organized in different groups. A group may
contain up to 10000 markers, so the program is suitable for drawing
circular representations of genomic sequences.
The program reads an input file containing the names and positions of
the genetic markers. You must write this file yourself (see Input File
Format below). Data for controlling the appearance of the markers may
also be added to this file.
Usage
Here is a sample session with cirdna
% cirdna -graph cps
Draw circular map of DNA constructs
Commands to the cirdna drawing program file [inputfile]: data.cirp
Draw a ruler [Y]:
Open : Open blocks
Filled : Filled blocks
Outline : Black border
Type of blocks [Filled]:
1 : In
2 : Out
Ticks inside or outside the circle [Out]:
1 : In
2 : Out
Text inside or outside the blocks [In]:
Created cirdna.ps
Go to the input files for this example
Go to the output files for this example
Command line arguments
Draw circular map of DNA constructs
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-infile] infile [inputfile] Commands to the cirdna drawing
program file
-[no]ruler boolean [Y] Draw a ruler
-blocktype menu [Filled] Type of blocks (Values: Open (Open
blocks); Filled (Filled blocks); Outline
(Black border))
-posticks selection [Out] Ticks inside or outside the circle
-posblocks selection [In] Text inside or outside the blocks
-graphout graph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tek, tekt, none, data, xterm, png, gif, pdf,
svg)
Additional (Optional) qualifiers:
-maxgroups integer [20] Maximum number of groups (Integer 1 or
more)
-maxlabels integer [10000] Maximum number of labels (Integer 1
or more)
-originangle float [90] Position in degrees of the molecule's
origin on the circle (Number from 0.000 to
360.000)
-[no]intersymbol boolean [Y] Horizontal junctions between blocks
-intercolour integer [1] Colour of junctions between blocks
(enter a colour number) (Integer from 0 to
15)
-interticks boolean [N] Horizontal junctions between ticks
-gapsize integer [500] Interval between ticks in the ruler
(Integer 0 or more)
-ticklines boolean [N] Vertical lines at the ruler's ticks
-textheight float [1.0] Height of text. Enter a number <1.0 or
>1.0 to decrease or increase the size,
respectively (Number 0.000 or more)
-textlength float [1.0] Length of text. Enter a number <1.0 or
>1.0 to decrease or increase the size,
respectively (Number 0.000 or more)
-tickheight float [1.0] Height of ticks. Enter a number <1.0
or >1.0 to decrease or increase the size,
respectively (Number 0.000 or more)
-blockheight float [1.0] Height of blocks. Enter a number <1.0
or >1.0 to decrease or increase the size,
respectively (Number 0.000 or more)
-rangeheight float [1.0] Height of range ends. Enter a number
<1.0 or >1.0 to decrease or increase the
size, respectively (Number 0.000 or more)
-gapgroup float [1.0] Space between groups. Enter a number
<1.0 or >1.0 to decrease or increase the
size, respectively (Number 0.000 or more)
-postext float [1.0] Space between text and ticks, blocks,
and ranges. Enter a number <1.0 or >1.0 to
decrease or increase the size, respectively
(Number 0.000 or more)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-graphout" associated qualifiers
-gprompt boolean Graph prompting
-gdesc string Graph description
-gtitle string Graph title
-gsubtitle string Graph subtitle
-gxtitle string Graph x axis title
-gytitle string Graph y axis title
-goutfile string Output file for non interactive displays
-gdirectory string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
Input file format
Blank lines in the input file are ignored.
The file is organized in several fields separated by one or more space
or TAB characters.
The first non-blank line gives the start position of the DNA fragment
to be drawn after the keyword 'Start'. The end position is on the
second line following the keyword 'End'.
Then, one or more groups (up to a maximum of 20) of genetic markers are
defined. Each group begins with a line consisting of the keyword
'group' and ends with a line consisting of the keyword 'endgroup'.
If desired, a group name can be given on the very next line but will
not be displayed (only for compatibilty with lindna).
Next, the individual markers (up to a maximum of 1000) of the group are
described. Each marker begins with a line consisting of the keyword
'label' and ends with a line consisting of the keyword 'endlabel'.
Do not start a new marker (by using a 'label' line) before you have
closed the previous marker (by using an 'endlabel' line). You must end
a previous marker specification before starting a new one. i.e. do not
overlap marker specifications in the input file.
For each marker, the line following the 'label' line describes the
marker. Three types of markers can be drawn: ticks, blocks, and ranges.
For a tick, the descriptive line begins with the keyword 'Tick',
followed by the position of the tick in the DNA fragment, and a number
from 0 to 15 specifying the color in which the tick will be drawn (a
list of available colors is given below). If desired, a name can be
written above the tick. This name must be given on the next line. If
more than one name are given (one name per line), only the first one
will be displayed.
For a block, the descriptive line begins with the keyword 'Block',
followed by the start and end positions of the block in the DNA
fragment, and the number of the block's color. If desired, a name can
be written above or inside the block. This name must be given on the
next line. If more than one name are given (one name per line), only
the first one will be displayed.
For a range, the descriptive line begins with the keyword 'Range',
followed by the start and end positions of the range in the DNA
fragment. Next on the line are the types of boundaries that are to be
drawn. The user can choose among '>', '<', '[', ']' and '|' for both
start and end boundaries. If none of these types is wanted for a given
boundary, then a point '.' must be entered. Next is the color number.
If desired, a name can be written above the range. This name must be
given on the next line. If more than one name are given (one name per
line), only the first one will be displayed.
For any type of markers, names will be written in the same color as the
marker. Also, try to avoid long names.
The colors defined in the PLPLOT graphics library are:
0 "BLACK", 1 "RED", 2 "YELLOW", 3 "GREEN", 4 "AQUAMARINE", 5 "PINK", 6
"WHEAT", 7 "GREY", 8 "BROWN", 9 "BLUE", 10 "BLUEVIOLET", 11 "CYAN", 12
"TURQUOISE", 13 "MAGENTA", 14 "SALMON", and 15 "WHITE".
This format can also be used for the program "lindna".
Input files for usage example
File: data.cirp
Start 1001
End 4270
group
label
Block 1011 1362 3
ex1
endlabel
label
Tick 1610 8
EcoR1
endlabel
label
Block 1647 1815 1
endlabel
label
Tick 2459 8
BamH1
endlabel
label
Block 4139 4258 3
ex2
endlabel
endgroup
group
label
Range 2541 2812 [ ] 5
Alu
endlabel
label
Range 3322 3497 > < 5
MER13
endlabel
endgroup
Output file format
Output files for usage example
Graphics File: cirdna.ps
[cirdna results] Output is to the specified graphics device.
Data files
None.
Notes
There are many options for controlling the appearance of the plot.
Mostly these are "additional qualifiers" and can be specified on the
command-line by using the corresponding flag, but will not normally be
prompted for. To be prompted for values for them, run the program with
the -options global qualifier.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with a status of 0.
Known bugs
None.
See also
Program name Description
abiview Display the trace in an ABI sequencer file
iep Calculate the isoelectric point of proteins
lindna Draw linear maps of DNA constructs
pepinfo Plot amino acid properties of a protein sequence in parallel
pepnet Draw a helical net for a protein sequence
pepwheel Draw a helical wheel diagram for a protein sequence
plotorf Plot potential open reading frames in a nucleotide sequence
prettyplot Draw a sequence alignment with pretty formatting
prettyseq Write a nucleotide sequence and its translation to file
remap Display restriction enzyme binding sites in a nucleotide sequence
showfeat Display features of a sequence in pretty format
showpep Display protein sequences with features in pretty format
sixpack Display a DNA sequence with 6-frame translation and ORFs
Author(s)
Nicolas Tourasse formerly at:
Biotechnology Center of Oslo
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
History
Written 1999 - Nicolas Tourasse
Updated (2002) - Nicolas Tourasse
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
|
