                                   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:6.5.6.0

   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
