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cirdna
Function
Draws circular maps of DNA constructs
Description
The program 'cirdna' draws circular maps of DNA constructs.
It uses the graphical shapes: 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 can be used to draw circular representations of genomic
sequences.
The program reads in one input file in which the user specifies the
names and positions of the genetic markers. In this file the user also
enters data for controlling the appearance of the markers.
A refined customization of the drawing can be achieved by running the
program with '-options' on the command line and changing the values of
the desired parameters.
Usage
Here is a sample session with cirdna
% cirdna -graph cps
Draws circular maps of DNA constructs
Commands to the lindna 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
Standard (Mandatory) qualifiers:
[-infile] infile [inputfile] Commands to the lindna 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,
tekt, tek, none, data, xterm, png, gif)
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 standard output
-filter boolean Read standard input, write 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. 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
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
None.
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 Reads ABI file and display the trace
lindna Draws linear maps of DNA constructs
pepnet Displays proteins as a helical net
pepwheel Shows protein sequences as helices
prettyplot Displays aligned sequences, with colouring and boxing
prettyseq Output sequence with translated ranges
remap Display sequence with restriction sites, translation etc
seealso Finds programs sharing group names
showalign Displays a multiple sequence alignment
showdb Displays information on the currently available databases
showfeat Show features of a sequence
showseq Display a sequence with features, translation etc
sixpack Display a DNA sequence with 6-frame translation and ORFs
textsearch Search sequence documentation. Slow, use SRS and Entrez!
Author(s)
Nicolas Tourasse (nicolas.tourasse biotek.uio.no)
Biotechnology Center of Oslo
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
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