
                                  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
Input file containing mapping data [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     Input file containing mapping data
   -[no]ruler          boolean    Draw a ruler
   -blocktype          menu       Type of blocks
   -posticks           selection  Ticks inside or outside the circle
   -posblocks          selection  Text inside or outside the blocks
   -graphout           graph      Graph type

   Additional (Optional) qualifiers:
   -maxgroups          integer    Maximum number of groups
   -maxlabels          integer    Maximum number of labels
   -originangle        float      Position in degrees of the molecule's origin
                                  on the circle
   -[no]intersymbol    boolean    Horizontal junctions between blocks
   -intercolour        integer    Colour of junctions between blocks (enter a
                                  colour number)
   -interticks         boolean    Horizontal junctions between ticks
   -gapsize            integer    Interval between ticks in the ruler
   -ticklines          boolean    Vertical lines at the ruler's ticks
   -textheight         float      Height of text. Enter a number <1.0 or >1.0
                                  to decrease or increase the size,
                                  respectively
   -textlength         float      Length of text. Enter a number <1.0 or >1.0
                                  to decrease or increase the size,
                                  respectively
   -tickheight         float      Height of ticks. Enter a number <1.0 or >1.0
                                  to decrease or increase the size,
                                  respectively
   -blockheight        float      Height of blocks. Enter a number <1.0 or
                                  >1.0 to decrease or increase the size,
                                  respectively
   -rangeheight        float      Height of range ends. Enter a number <1.0 or
                                  >1.0 to decrease or increase the size,
                                  respectively
   -gapgroup           float      Space between groups. Enter a number <1.0 or
                                  >1.0 to decrease or increase the size,
                                  respectively
   -postext            float      Space between text and ticks, blocks, and
                                  ranges. Enter a number <1.0 or >1.0 to
                                  decrease or increase the size, respectively

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-graphout" associated qualifiers
   -gprompt             boolean    Graph prompting
   -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 deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-infile]
   (Parameter 1) Input file containing mapping data Input file inputfile
   -[no]ruler Draw a ruler Boolean value Yes/No Yes
   -blocktype Type of blocks
   Open    (Open blocks)
   Filled  (Filled blocks)
   Outline (Black border)
   Filled
   -posticks Ticks inside or outside the circle Choose from selection
   list of values Out
   -posblocks Text inside or outside the blocks Choose from selection
   list of values In
   -graphout Graph type EMBOSS has a list of known devices, including
   postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows,
   x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm,
   png, xml EMBOSS_GRAPHICS value, or x11
   Additional (Optional) qualifiers Allowed values Default
   -maxgroups Maximum number of groups Integer 1 or more 20
   -maxlabels Maximum number of labels Integer 1 or more 10000
   -originangle Position in degrees of the molecule's origin on the
   circle Number from 0.000 to 360.000 90
   -[no]intersymbol Horizontal junctions between blocks Boolean value
   Yes/No Yes
   -intercolour Colour of junctions between blocks (enter a colour
   number) Integer from 0 to 15 1
   -interticks Horizontal junctions between ticks Boolean value Yes/No No
   -gapsize Interval between ticks in the ruler Integer 0 or more 500
   -ticklines Vertical lines at the ruler's ticks Boolean value Yes/No No
   -textheight Height of text. Enter a number <1.0 or >1.0 to decrease or
   increase the size, respectively Number 0.000 or more 1.0
   -textlength Length of text. Enter a number <1.0 or >1.0 to decrease or
   increase the size, respectively Number 0.000 or more 1.0
   -tickheight Height of ticks. Enter a number <1.0 or >1.0 to decrease
   or increase the size, respectively Number 0.000 or more 1.0
   -blockheight Height of blocks. Enter a number <1.0 or >1.0 to decrease
   or increase the size, respectively Number 0.000 or more 1.0
   -rangeheight Height of range ends. Enter a number <1.0 or >1.0 to
   decrease or increase the size, respectively Number 0.000 or more 1.0
   -gapgroup Space between groups. Enter a number <1.0 or >1.0 to
   decrease or increase the size, respectively Number 0.000 or more 1.0
   -postext 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 1.0
   Advanced (Unprompted) qualifiers Allowed values Default
   (none)

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 a sequence with restriction cut 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 text. SRS and Entrez are
   faster!

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
