CSC

 
 
Tehdyt toimenpiteet
EMBOSS: cirdna
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

Draws circular maps 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 
Draws circular maps 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 

Draws circular maps of DNA constructs
Version: EMBOSS:6.4.0.0

   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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-infile]
(Parameter 1)		 infile Commands to the cirdna drawing program file Input file inputfile
-[no]ruler boolean Draw a ruler Boolean value Yes/No Yes
-blocktype list Type of blocks
Open (Open blocks)
Filled (Filled blocks)
Outline (Black border)
 Filled
-posticks selection Ticks inside or outside the circle Choose from selection list of values Out
-posblocks selection Text inside or outside the blocks Choose from selection list of values In
-graphout graph Graph type EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers
-maxgroups integer Maximum number of groups Integer 1 or more 20
-maxlabels integer Maximum number of labels Integer 1 or more 10000
-originangle float Position in degrees of the molecule's origin on the circle Number from 0.000 to 360.000 90
-[no]intersymbol boolean Horizontal junctions between blocks Boolean value Yes/No Yes
-intercolour integer Colour of junctions between blocks (enter a colour number) Integer from 0 to 15 1
-interticks boolean Horizontal junctions between ticks Boolean value Yes/No No
-gapsize integer Interval between ticks in the ruler Integer 0 or more 500
-ticklines boolean Vertical lines at the ruler's ticks Boolean value Yes/No No
-textheight float 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 float 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 float 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 float 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 float 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 float 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 float 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
(none)
Associated qualifiers
"-graphout" associated graph qualifiers
-gprompt boolean Graph prompting Boolean value Yes/No N
-gdesc string Graph description Any string Circular DNA map
-gtitle string Graph title Any string  
-gsubtitle string Graph subtitle Any string  
-gxtitle string Graph x axis title Any string  
-gytitle string Graph y axis title Any string  
-goutfile string Output file for non interactive displays Any string  
-gdirectory string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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 Draws 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 Displays 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 © 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