lindna

 

Function

Draws linear maps of DNA constructs

Description

The program 'lindna' draws linear 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.

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 lindna


% lindna -graph cps 
Draws linear maps of DNA constructs
Input file [inputfile]: ../../data/data.linp
do you want a ruler [Y]: 
      1 : Open
      2 : Filled
      3 : Outline
type of blocks (enter Open, Filled, or Outline) [Filled]: 

Created lindna.ps

Go to the input files for this example
Go to the output files for this example

Command line arguments

   Mandatory qualifiers:
   -graphout           graph      Graph type
   -inputfile          infile     input file containing mapping data
   -[no]ruler          boolean    do you want a ruler
   -blocktype          selection  type of blocks: Open, Filled, or Outline.
                                  Option 'Outline' draws filled blocks
                                  surrounded by a black border

   Optional qualifiers:
   -intersymbol        selection  type of junctions between blocks
   -intercolour        integer    colour of junctions between blocks (enter a
                                  colour number)
   -interticks         boolean    do you want horizontal junctions between
                                  ticks
   -gapsize            integer    interval between ticks in the ruler (enter
                                  an integer)
   -ticklines          boolean    do you want vertical lines at the ruler's
                                  ticks
   -textheight         float      height of text. Enter a number <1 or >1 to
                                  decrease or increase the size, respectively
   -textlength         float      length of text. Enter a number <1 or >1 to
                                  decrease or increase the size, respectively
   -margin             float      width of left margin. This is the region
                                  left to the groups where the names of the
                                  groups are displayed. Enter a number <1 or
                                  >1 to decrease or increase the size,
                                  respectively
   -tickheight         float      height of ticks. Enter a number <1 or >1 to
                                  decrease or increase the size, respectively
   -blockheight        float      height of blocks. Enter a number <1 or >1 to
                                  decrease or increase the size, respectively
   -rangeheight        float      height of range ends. Enter a number <1 or
                                  >1 to decrease or increase the size,
                                  respectively
   -gapgroup           float      space between groups. Enter a number <1 or
                                  >1 to decrease or increase the size,
                                  respectively
   -postext            float      space between text and ticks, blocks, and
                                  ranges. Enter a number <1 or >1 to decrease
                                  or increase the size, respectively

   Advanced qualifiers: (none)
   General qualifiers:
  -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


Mandatory qualifiers Allowed values Default
-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 EMBOSS_GRAPHICS value, or x11
-inputfile input file containing mapping data Input file inputfile
-[no]ruler do you want a ruler Boolean value Yes/No Yes
-blocktype type of blocks: Open, Filled, or Outline. Option 'Outline' draws filled blocks surrounded by a black border Choose from selection list of values Filled
Optional qualifiers Allowed values Default
-intersymbol type of junctions between blocks Choose from selection list of values Straight
-intercolour colour of junctions between blocks (enter a colour number) Integer from 0 to 15 1
-interticks do you want horizontal junctions between ticks Boolean value Yes/No No
-gapsize interval between ticks in the ruler (enter an integer) Integer 0 or more 500
-ticklines do you want vertical lines at the ruler's ticks Boolean value Yes/No No
-textheight height of text. Enter a number <1 or >1 to decrease or increase the size, respectively Any numeric value 1
-textlength length of text. Enter a number <1 or >1 to decrease or increase the size, respectively Any numeric value 1
-margin width of left margin. This is the region left to the groups where the names of the groups are displayed. Enter a number <1 or >1 to decrease or increase the size, respectively Number 0.000 or more 1
-tickheight height of ticks. Enter a number <1 or >1 to decrease or increase the size, respectively Any numeric value 1
-blockheight height of blocks. Enter a number <1 or >1 to decrease or increase the size, respectively Any numeric value 1
-rangeheight height of range ends. Enter a number <1 or >1 to decrease or increase the size, respectively Any numeric value 1
-gapgroup space between groups. Enter a number <1 or >1 to decrease or increase the size, respectively Any numeric value 1
-postext space between text and ticks, blocks, and ranges. Enter a number <1 or >1 to decrease or increase the size, respectively Any numeric value 1
Advanced qualifiers Allowed values Default
(none)

Input file format

Input files for usage example

File: ../../data/data.linp

Start	1001
End	4270

group
exons
label
Block	1011	1362	3	H
ex1
endlabel
label
Tick	1610	8	H
EcoR1
endlabel
label
Block	1647	1815	1	H
endlabel
label
Tick	2459	8	H
BamH1
endlabel
label
Block	4139	4258	3	H
ex2
endlabel
endgroup

group
repeat-regions
label
Range	2541	2812	[	]	5	V
Alu
endlabel
label
Range	3322	3497	>	<	5	V
MER13
endlabel

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. Spaces and tabulations are allowed but only the first 20 characters of that name (including spaces) will be displayed.

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, one or more names can be written above the tick. In this case an optional letter H or V should be added to the line. H or V indicate whether the text will be horizontal or vertical, respectively. If no letter is specified, H is assumed by default. A list of one or more names can be given on the next lines with one name per line.

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, one or more names can be written above the block. Names are given on the following lines. An optional letter H or V can be added to the end of the descriptive line to specify the orientation of the name(s).

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, one or more names can be written above the range. Names are given on the following lines. An optional letter H or V can be added to the end of the descriptive line to specify the orientation of the name(s).

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 "cirdna".

Output file format

Output is to the specified graphics device.

Output files for usage example

Graphics File: lindna.ps

[lindna results]

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 nameDescription
abiviewReads ABI file and display the trace
cirdnaDraws circular maps of DNA constructs
pepnetDisplays proteins as a helical net
pepwheelShows protein sequences as helices
prettyplotDisplays aligned sequences, with colouring and boxing
prettyseqOutput sequence with translated ranges
remapDisplay a sequence with restriction cut sites, translation etc
seealsoFinds programs sharing group names
showalignDisplays a multiple sequence alignment
showdbDisplays information on the currently available databases
showfeatShow features of a sequence
showseqDisplay a sequence with features, translation etc
sixpackDisplay a DNA sequence with 6-frame translation and ORFs
textsearchSearch sequence documentation text. SRS and Entrez are faster!

cirdna plots representations of circular DNA.

Author(s)

This application was written by Nicolas Tourasse (nicolas.tourasse@biotek.uio.no) at the Biotechnology Center of Oslo.

History

Written (2000) - 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